diff --git a/CHANGELOG.md b/CHANGELOG.md index fc243f3..b56499b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns. +- [#127] (https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem +- [#128] (https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics ### `Fixed` diff --git a/CITATIONS.md b/CITATIONS.md index 208cfa1..36704d9 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -28,6 +28,16 @@ - [Seqtk](https://github.com/lh3/seqtk) +- [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962) + +> Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041 + +- [SAMTOOLS](https://academic.oup.com/bioinformatics/article/25/16/2078/204688) + +> Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008 + +- [Picard Tools](https://broadinstitute.github.io/picard/) + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) diff --git a/README.md b/README.md index 1659744..1f1396c 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,11 @@ 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk)) 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)) +4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools)) +5. Create FASTA index ([`SAMtools`](http://github.com/samtools)) +6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)) +7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage diff --git a/conf/modules.config b/conf/modules.config index e90c730..31a9112 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,11 +18,11 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: SEQTK_SAMPLE { + withName: 'SEQTK_SAMPLE' { ext.args = '-s100' } - withName: FASTQC { + withName: 'FASTQC' { ext.args = '--quiet' } @@ -42,6 +42,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + withName: 'BWAMEM2_MEM' { publishDir = [ path: { "${params.outdir}/bwamem2_mem" }, @@ -50,6 +51,33 @@ process { ] } + withName: 'PICARD_COLLECTMULTIPLEMETRICS' { + ext.args = '' + publishDir = [ + path: { "${params.outdir}/picard_collectmultiplemetrics" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'SAMTOOLS_FAIDX' { + ext.args = '' + publishDir = [ + path: { "${params.outdir}/samtools_faidx" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'SAMTOOLS_INDEX' { + ext.args = '' + publishDir = [ + path: { "${params.outdir}/samtools_index" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: 'MULTIQC_GLOBAL' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/seqinspector_v1.0_stage_resources.config b/conf/seqinspector_v1.0_stage_resources.config new file mode 100644 index 0000000..c7f4f64 --- /dev/null +++ b/conf/seqinspector_v1.0_stage_resources.config @@ -0,0 +1,72 @@ +process { + + + // TODO nf-core: Check the defaults for all processes + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } + + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + maxRetries = 2 + maxErrors = '-1' + + + // Subsampling reads + withName: 'SEQTK_SAMPLE' { + cpus = 6 + memory = { 4.GB * task.attempt } + time = { 4.h * task.attempt } + } + + // Quality control + withName: 'FASTQC' { + cpus = 2 + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } + } + withName: 'SEQFU_STATS' { + cpus = 6 + memory = { 4.GB * task.attempt } + time = { 4.h * task.attempt } + } + withName: 'FASTQSCREEN_FASTQSCREEN' { + cpus = 6 + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } + } + + // Reference genome processing + withName: 'BWAMEM2_INDEX' { + cpus = 12 + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } + } + withName: 'BWAMEM2_MEM' { + cpus = 6 + memory = { 35.GB * task.attempt } + time = { 16.h * task.attempt } + } + withName: 'SAMTOOLS_INDEX' { + cpus = 6 + memory = { 4.GB * task.attempt } + time = { 4.h * task.attempt } + } + withName: 'SAMTOOLS_FAIDX' { + cpus = 6 + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } + } + // Picard metrics + withName: 'PICARD_COLLECTMULTIPLEMETRICS' { + cpus = 4 + memory = { 8.GB * task.attempt } + time = { 4.h * task.attempt } + } + + // MultiQC aggregation + withName: 'MULTIQC_GLOBAL|MULTIQC_PER_TAG' { + cpus = 4 + memory = { 4.GB * task.attempt } + time = { 4.h * task.attempt } + } +} diff --git a/main.nf b/main.nf index 73c21f0..56bbfec 100644 --- a/main.nf +++ b/main.nf @@ -36,7 +36,6 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_seqi // WORKFLOW: Run main analysis pipeline depending on type of input // workflow NFCORE_SEQINSPECTOR { - take: samplesheet // channel: samplesheet read in from --input @@ -46,13 +45,14 @@ workflow NFCORE_SEQINSPECTOR { // WORKFLOW: Run pipeline // - SEQINSPECTOR ( - samplesheet + SEQINSPECTOR( + samplesheet, + params.fasta, ) - emit: - global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html - grouped_reports = SEQINSPECTOR.out.grouped_reports // channel: /path/to/multiqc_report.html + emit: + global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html + grouped_reports = SEQINSPECTOR.out.grouped_reports // channel: /path/to/multiqc_report.html } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -62,14 +62,12 @@ workflow NFCORE_SEQINSPECTOR { workflow { - main: - // // SUBWORKFLOW: Run initialisation tasks // - PIPELINE_INITIALISATION ( + PIPELINE_INITIALISATION( params.version, params.validate_params, params.monochrome_logs, @@ -84,13 +82,13 @@ workflow { // // WORKFLOW: Run main workflow // - NFCORE_SEQINSPECTOR ( - PIPELINE_INITIALISATION.out.samplesheet, + NFCORE_SEQINSPECTOR( + PIPELINE_INITIALISATION.out.samplesheet ) // // SUBWORKFLOW: Run completion tasks // - PIPELINE_COMPLETION ( + PIPELINE_COMPLETION( params.email, params.email_on_fail, params.plaintext_email, @@ -119,9 +117,3 @@ def getGenomeAttribute(attribute) { } return null } - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ diff --git a/nextflow.config b/nextflow.config index b49ba16..2397152 100644 --- a/nextflow.config +++ b/nextflow.config @@ -19,6 +19,7 @@ params { igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false sort_bam = true + bwa_index = null // Fastqscreen options fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv" diff --git a/nextflow_schema.json b/nextflow_schema.json index 52bb676..41ce805 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -214,7 +214,8 @@ "modules_testdata_base_path": { "type": "string", "description": "Base path / URL for data used in the modules", - "hidden": true + "hidden": true, + "default": "s3://ngi-igenomes/testdata/nf-core/modules/" }, "multiqc_config": { "type": "string", @@ -282,5 +283,10 @@ { "$ref": "#/$defs/generic_options" } - ] + ], + "properties": { + "bwa_index": { + "type": "string" + } + } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index a6d9804..5633429 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-11-07T09:27:51+00:00", - "description": "

\n \n \n \"nf-core/seqinspector\"\n \n

\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-11-07T10:20:35+00:00", + "description": "

\n \n \n \"nf-core/seqinspector\"\n \n

\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))\n4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))\n5. Create FASTA index ([`SAMtools`](http://github.com/samtools))\n6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b" + "@id": "#b66d14a8-59db-4642-b2a8-9ae193c96008" } ], "name": "nf-core/seqinspector" @@ -127,21 +127,24 @@ "ComputationalWorkflow" ], "creator": [ + { + "@id": "https://orcid.org/0000-0003-2702-1103" + }, { "@id": "https://orcid.org/0000-0003-1675-0677" }, { - "@id": "https://orcid.org/0000-0003-2702-1103" + "@id": "https://orcid.org/0009-0004-5536-7210" }, { - "@id": "#89784800+kedhammar@users.noreply.github.com" + "@id": "#max.u.garcia@gmail.com" }, { - "@id": "https://orcid.org/0009-0004-5536-7210" + "@id": "#89784800+kedhammar@users.noreply.github.com" } ], "dateCreated": "", - "dateModified": "2025-11-07T10:27:51Z", + "dateModified": "2025-11-07T11:20:35Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -182,11 +185,11 @@ "version": "!>=25.04.0" }, { - "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b", + "@id": "#b66d14a8-59db-4642-b2a8-9ae193c96008", "@type": "TestSuite", "instance": [ { - "@id": "#56ac1623-4e68-4598-9703-f769123f08c5" + "@id": "#4a975f08-07ae-4c90-84d2-cefcf6352c88" } ], "mainEntity": { @@ -195,7 +198,7 @@ "name": "Test suite for nf-core/seqinspector" }, { - "@id": "#56ac1623-4e68-4598-9703-f769123f08c5", + "@id": "#4a975f08-07ae-4c90-84d2-cefcf6352c88", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/seqinspector", "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml", @@ -323,12 +326,6 @@ "name": "nf-core", "url": "https://nf-co.re/" }, - { - "@id": "https://orcid.org/0000-0003-1675-0677", - "@type": "Person", - "email": "mahesh.binzer-panchal@nbis.se", - "name": "Mahesh Binzer-Panchal" - }, { "@id": "https://orcid.org/0000-0003-2702-1103", "@type": "Person", @@ -336,16 +333,28 @@ "name": "Adrien Coulier" }, { - "@id": "#89784800+kedhammar@users.noreply.github.com", + "@id": "https://orcid.org/0000-0003-1675-0677", "@type": "Person", - "email": "89784800+kedhammar@users.noreply.github.com", - "name": "Alfred Kedhammar" + "email": "mahesh.binzer-panchal@nbis.se", + "name": "Mahesh Binzer-Panchal" }, { "@id": "https://orcid.org/0009-0004-5536-7210", "@type": "Person", "email": "agrimabhatt@n141-p117.eduroam.kth.se", "name": "Agrima Bhatt" + }, + { + "@id": "#max.u.garcia@gmail.com", + "@type": "Person", + "email": "max.u.garcia@gmail.com", + "name": "Maxime U Garcia" + }, + { + "@id": "#89784800+kedhammar@users.noreply.github.com", + "@type": "Person", + "email": "89784800+kedhammar@users.noreply.github.com", + "name": "Alfred Kedhammar" } ] } \ No newline at end of file diff --git a/tests/.nftignore b/tests/.nftignore index e509839..ee3b401 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -11,4 +11,11 @@ multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_software_versions.t multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_sources.txt multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/{global_report,group_reports/*}/multiqc_report.html +picard_collectmultiplemetrics/*.pdf +picard_collectmultiplemetrics/*_metrics +picard_collectmultiplemetrics/alignment_summary_metrics +picard_collectmultiplemetrics/base_distribution_by_cycle_metrics +picard_collectmultiplemetrics/quality_by_cycle_metrics +picard_collectmultiplemetrics/quality_distribution_metrics +picard_collectmultiplemetrics/*_summary_metrics pipeline_info/*.{html,json,txt,yml} diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap index 885a1e7..9851e44 100644 --- a/tests/MiSeq.main.nf.test.snap +++ b/tests/MiSeq.main.nf.test.snap @@ -47,6 +47,15 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { "seqfu": "1.20.3" }, @@ -93,9 +102,26 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -110,6 +136,16 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -124,6 +160,16 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -138,10 +184,34 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", + "samtools_index", + "samtools_index/SAMPLE_SINGLE_END_1.bam.bai", "seqfu_stats", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt" @@ -168,7 +238,27 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607", "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99", + "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942", + "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703", "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703", + "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0", + "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627", + "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023", + "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9", + "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af", + "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876", + "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb", "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39" ] @@ -177,7 +267,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:23:17.145777453" + "timestamp": "2025-11-07T11:14:40.189991111" }, "Miseq data test (skip fastqc)": { "content": [ @@ -192,6 +282,15 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { "seqfu": "1.20.3" }, @@ -223,25 +322,86 @@ "multiqc/global_report/multiqc_data/multiqc_citations.txt", "multiqc/global_report/multiqc_data/multiqc_data.json", "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", + "samtools_index", + "samtools_index/SAMPLE_SINGLE_END_1.bam.bai", "seqfu_stats", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt" @@ -258,7 +418,27 @@ "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99", + "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942", + "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703", "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703", + "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0", + "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627", + "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023", + "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9", + "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af", + "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876", + "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb", "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39" ] @@ -267,6 +447,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:47:45.83823672" + "timestamp": "2025-11-07T11:15:17.347135189" } } \ No newline at end of file diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap index 10a9b11..728ed4d 100644 --- a/tests/MiSeq_PairedEnd.main.nf.test.snap +++ b/tests/MiSeq_PairedEnd.main.nf.test.snap @@ -15,6 +15,15 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { "seqfu": "1.20.3" }, @@ -76,9 +85,27 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -92,6 +119,18 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -105,6 +144,18 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -118,6 +169,18 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", "multiqc/group_reports", @@ -141,9 +204,27 @@ "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Reads.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/Bpacificus/multiqc_plots", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -157,6 +238,18 @@ "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -170,6 +263,18 @@ "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png", "multiqc/group_reports/Bpacificus/multiqc_plots/svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -183,10 +288,45 @@ "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/Bpacificus/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", + "samtools_index", + "samtools_index/SAMPLE_PAIRED_END_1_1.bam.bai", + "samtools_index/SAMPLE_PAIRED_END_2_2.bam.bai", "seqfu_stats", "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv", "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt", @@ -222,7 +362,25 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5", "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb", + "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f", + "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0", "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0", + "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712", + "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792", + "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f", + "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170", + "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d", + "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6", + "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e", + "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d", "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd", "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b", "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445", @@ -236,7 +394,29 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5", "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb", + "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f", + "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0", "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0", + "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712", + "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792", + "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f", + "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170", + "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d", + "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6", + "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e", + "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464", + "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210", "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6", "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c", "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799", @@ -247,6 +427,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:24:43.782493978" + "timestamp": "2025-11-07T11:16:28.36937489" } } \ No newline at end of file diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap index f2985aa..50a55e5 100644 --- a/tests/NovaSeq6000.main.nf.test.snap +++ b/tests/NovaSeq6000.main.nf.test.snap @@ -15,6 +15,15 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { "seqfu": "1.20.3" }, @@ -86,9 +95,26 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -104,6 +130,16 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -119,6 +155,16 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -134,6 +180,16 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", "multiqc/group_reports", @@ -159,9 +215,26 @@ "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_plots", "multiqc/group_reports/group1/multiqc_plots/pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -177,6 +250,16 @@ "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group1/multiqc_plots/png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -192,6 +275,16 @@ "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group1/multiqc_plots/svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -207,6 +300,16 @@ "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group1/multiqc_report.html", "multiqc/group_reports/group2", @@ -231,9 +334,26 @@ "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_plots", "multiqc/group_reports/group2/multiqc_plots/pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -249,6 +369,16 @@ "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group2/multiqc_plots/png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -264,6 +394,16 @@ "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group2/multiqc_plots/svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -279,6 +419,16 @@ "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group2/multiqc_report.html", "multiqc/group_reports/lane1", @@ -303,9 +453,26 @@ "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_plots", "multiqc/group_reports/lane1/multiqc_plots/pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -321,6 +488,16 @@ "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/lane1/multiqc_plots/png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -336,6 +513,16 @@ "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/lane1/multiqc_plots/svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -351,6 +538,16 @@ "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/lane1/multiqc_report.html", "multiqc/group_reports/test", @@ -375,9 +572,26 @@ "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_plots", "multiqc/group_reports/test/multiqc_plots/pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -393,6 +607,16 @@ "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/test/multiqc_plots/png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -408,6 +632,16 @@ "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/test/multiqc_plots/png/seqfu.png", "multiqc/group_reports/test/multiqc_plots/svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -423,10 +657,70 @@ "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/test/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", + "samtools_index", + "samtools_index/Sample1_1.bam.bai", + "samtools_index/Sample23_3.bam.bai", + "samtools_index/SampleA_2.bam.bai", + "samtools_index/Undetermined_5.bam.bai", + "samtools_index/sampletest_4.bam.bai", "seqfu_stats", "seqfu_stats/Sample1_1_seqfu.tsv", "seqfu_stats/Sample1_1_seqfu_mqc.txt", @@ -474,7 +768,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638", "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e", + "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd", + "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42", + "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df", "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42", + "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df", + "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4", + "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224", + "picard_base_distribution_by_cycle__Adenine.txt:md5,61c7df03f74846ffa484a59fcccc7b9e", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,b4504bbb9ad72796703873f2d957977a", + "picard_base_distribution_by_cycle__Guanine.txt:md5,1d38466783ea51bf0c7be5bceaff4d43", + "picard_base_distribution_by_cycle__Thymine.txt:md5,1b13c9b64042839a3bc65a8553e5ba24", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,75aee7627205c6513389d7a52e7a383b", + "picard_quality_by_cycle.txt:md5,4850a9230f9be5af67f3d934602df440", + "picard_quality_score_distribution.txt:md5,17f8498a5b18cea0eb4796a6e12b8e36", "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994", "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84", "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289", @@ -489,7 +800,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff", "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a", + "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b", + "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5", + "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e", "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5", + "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e", + "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c", + "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480", + "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2", + "picard_base_distribution_by_cycle__Guanine.txt:md5,85a9172769830b4169f214c335f44fdc", + "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94", + "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734", + "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805", "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740", "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53", "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c", @@ -504,7 +832,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d", "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7", + "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5", + "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f", + "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620", "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f", + "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620", + "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d", + "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f", + "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b", + "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5", + "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c", + "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d", + "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802", "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06", "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1", "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01", @@ -519,7 +864,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc", "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4", + "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64", + "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7", + "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5", "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7", + "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5", + "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b", + "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2", + "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97", + "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b", + "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c", + "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1", + "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a", "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d", "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c", "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa", @@ -534,7 +896,31 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5", "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4", + "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f", + "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5", + "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49", "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5", + "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49", + "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9", + "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e", + "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb", + "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc", + "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf", + "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b", + "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869", "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6", "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676", @@ -551,6 +937,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:25:42.576692828" + "timestamp": "2025-11-07T11:17:47.210647423" } } \ No newline at end of file diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap index a539c84..cb93620 100644 --- a/tests/NovaSeq6000.main_subsample.nf.test.snap +++ b/tests/NovaSeq6000.main_subsample.nf.test.snap @@ -15,6 +15,15 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { "seqfu": "1.20.3" }, @@ -89,9 +98,26 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -107,6 +133,16 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -122,6 +158,16 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -137,6 +183,16 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", "multiqc/group_reports", @@ -162,9 +218,26 @@ "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_plots", "multiqc/group_reports/group1/multiqc_plots/pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -180,6 +253,16 @@ "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group1/multiqc_plots/png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -195,6 +278,16 @@ "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group1/multiqc_plots/svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -210,6 +303,16 @@ "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group1/multiqc_report.html", "multiqc/group_reports/group2", @@ -234,9 +337,26 @@ "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_plots", "multiqc/group_reports/group2/multiqc_plots/pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -252,6 +372,16 @@ "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group2/multiqc_plots/png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -267,6 +397,16 @@ "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group2/multiqc_plots/svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -282,6 +422,16 @@ "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group2/multiqc_report.html", "multiqc/group_reports/lane1", @@ -306,9 +456,26 @@ "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_plots", "multiqc/group_reports/lane1/multiqc_plots/pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -324,6 +491,16 @@ "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/lane1/multiqc_plots/png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -339,6 +516,16 @@ "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/lane1/multiqc_plots/svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -354,6 +541,16 @@ "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/lane1/multiqc_report.html", "multiqc/group_reports/test", @@ -378,9 +575,26 @@ "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_plots", "multiqc/group_reports/test/multiqc_plots/pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -396,6 +610,16 @@ "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/test/multiqc_plots/png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -411,6 +635,16 @@ "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/test/multiqc_plots/png/seqfu.png", "multiqc/group_reports/test/multiqc_plots/svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -426,10 +660,70 @@ "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/test/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", + "samtools_index", + "samtools_index/Sample1_1.bam.bai", + "samtools_index/Sample23_3.bam.bai", + "samtools_index/SampleA_2.bam.bai", + "samtools_index/Undetermined_5.bam.bai", + "samtools_index/sampletest_4.bam.bai", "seqfu_stats", "seqfu_stats/Sample1_1_seqfu.tsv", "seqfu_stats/Sample1_1_seqfu_mqc.txt", @@ -483,7 +777,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638", "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517", + "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa", + "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd", + "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6", "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd", + "picard_QualityScoreDistribution_histogram.txt:md5,792755ee794d375b85a57f58d879f0c6", + "picard_alignment_readlength_plot.txt:md5,ebd1ff06394bd202b8190c46d560bc95", + "picard_alignment_summary.txt:md5,e507eccfa0a05b20705f99a3619dde29", + "picard_base_distribution_by_cycle__Adenine.txt:md5,597d0fd368eab8a21cd7f4a92965ecf6", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,ade1d92e5e6d3bfefd3695f103079b6c", + "picard_base_distribution_by_cycle__Guanine.txt:md5,af525e84f95ceb4b8496f734db2420fb", + "picard_base_distribution_by_cycle__Thymine.txt:md5,8b5ada27023f2545792fabbb69a07067", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,a472bba4490d7189df23f6b38a554448", + "picard_quality_by_cycle.txt:md5,83d68b4049173f8c9a37f58f1276adc1", + "picard_quality_score_distribution.txt:md5,42c08c8a51230d9ecccdad416c06f59c", "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994", "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02", "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60", @@ -498,7 +809,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff", "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa", + "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c", + "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876", + "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4", "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876", + "picard_QualityScoreDistribution_histogram.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4", + "picard_alignment_readlength_plot.txt:md5,5aed5e7c1395a537bdce7163c93781bd", + "picard_alignment_summary.txt:md5,9d0d003456e08f78701e876d0238b5a6", + "picard_base_distribution_by_cycle__Adenine.txt:md5,73e910febe1ea4d08a9f4e49d6c10615", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,092e732bb44842f2da5416de158c1cc5", + "picard_base_distribution_by_cycle__Guanine.txt:md5,e81495fde738e2954483195fd0ccfb04", + "picard_base_distribution_by_cycle__Thymine.txt:md5,ed9ad958081a904a5584757f87b29eb2", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,2b4526a0b0977ebd7fbe326c6d51cf19", + "picard_quality_by_cycle.txt:md5,d53617c495e81e011996cd4e9f755e0a", + "picard_quality_score_distribution.txt:md5,05f9e89733e43b81acf593efc1a56180", "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740", "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53", "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1", @@ -513,7 +841,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d", "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8", + "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838", + "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792", + "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf", "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792", + "picard_QualityScoreDistribution_histogram.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf", + "picard_alignment_readlength_plot.txt:md5,72e0094fcd2546bee02a7ac65a3ea218", + "picard_alignment_summary.txt:md5,19586495e6d7904a2a4a7eb9ba17a412", + "picard_base_distribution_by_cycle__Adenine.txt:md5,a825de2b668791e58f6a4078e0b31483", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,59633faead8aa9027883481b0c7e22af", + "picard_base_distribution_by_cycle__Guanine.txt:md5,f02153a346f7e24f200bf06af2293352", + "picard_base_distribution_by_cycle__Thymine.txt:md5,0725af81caa647ec22050c573dfe8cb0", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,3536e6dcc7c7ed972b02d2945da75cb7", + "picard_quality_by_cycle.txt:md5,be127a96dd68c14077548d36c0507dc3", + "picard_quality_score_distribution.txt:md5,9e27b097f10cb9a9a95a3445b220d104", "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06", "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26", "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e", @@ -528,7 +873,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc", "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7", + "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c", + "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e", + "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b", "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e", + "picard_QualityScoreDistribution_histogram.txt:md5,dd5abab3a7141654fffa3946c50a039b", + "picard_alignment_readlength_plot.txt:md5,e5d397c216a0911a73dff5550fa7b1d7", + "picard_alignment_summary.txt:md5,ef16e8dbab178f44deebe0f4d321097b", + "picard_base_distribution_by_cycle__Adenine.txt:md5,8ada743b028ec78996f9dc40f1922941", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,c97859ee1641de9bff58dbd1e82fff20", + "picard_base_distribution_by_cycle__Guanine.txt:md5,ea86115ef2ca4ff4922486ceb6c6e1e8", + "picard_base_distribution_by_cycle__Thymine.txt:md5,07a3f1e6b1ed2bc55128fc2a0f46eb92", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,67ee93606c468a7eea7818b2f4b3389f", + "picard_quality_by_cycle.txt:md5,974b3baed160e9643f493df1d0ad5000", + "picard_quality_score_distribution.txt:md5,869d69ae4e243f0669f63b489563e4f1", "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d", "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c", "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18", @@ -543,7 +905,31 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5", "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c", + "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393", + "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba", + "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27", "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba", + "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27", + "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c", + "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c", + "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1", + "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e", + "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b", + "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc", + "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869", "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6", "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676", @@ -565,6 +951,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:26:40.559862265" + "timestamp": "2025-11-07T11:18:58.975063972" } } \ No newline at end of file diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config index 526df7b..46e9c09 100644 --- a/tests/PromethION.main.nf.test.config +++ b/tests/PromethION.main.nf.test.config @@ -6,4 +6,5 @@ params { input = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv' genome = 'EB1' skip_tools = 'bwamem2_index,bwamem2_mem' + } diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index 5aaa34f..a90115f 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -1,4 +1,4 @@ -include { samplesheetToList } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6,15 +6,18 @@ include { samplesheetToList } from 'plugin/nf-schema' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample/main' -include { FASTQC } from '../modules/nf-core/fastqc/main' +include { BWAMEM2_INDEX } from '../modules/nf-core/bwamem2/index' +include { BWAMEM2_MEM } from '../modules/nf-core/bwamem2/mem' +include { FASTQC } from '../modules/nf-core/fastqc' +include { FASTQSCREEN_FASTQSCREEN } from '../modules/nf-core/fastqscreen/fastqscreen' +include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics' +include { SAMTOOLS_FAIDX } from '../modules/nf-core/samtools/faidx' +include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index' include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats' -include { FASTQSCREEN_FASTQSCREEN } from '../modules/nf-core/fastqscreen/fastqscreen/main' -include { BWAMEM2_INDEX } from '../modules/nf-core/bwamem2/index/main' -include { BWAMEM2_MEM } from '../modules/nf-core/bwamem2/mem/main' +include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample' -include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc/main' -include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc/main' +include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc' +include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc' include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' @@ -28,29 +31,37 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfco */ workflow SEQINSPECTOR { - take: - ch_samplesheet // channel: samplesheet read in from --input + ch_samplesheet // channel: samplesheet read in from --input + fasta_file main: skip_tools = params.skip_tools ? params.skip_tools.split(',') : [] - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() - ch_multiqc_extra_files = Channel.empty() - ch_multiqc_reports = Channel.empty() + ch_versions = channel.empty() + ch_multiqc_files = channel.empty() + ch_multiqc_extra_files = channel.empty() + ch_multiqc_reports = channel.empty() + + // Initialize all channels that might be used later + ch_bwamem2_index = channel.empty() + ch_bwamem2_mem = channel.empty() + ch_samtools_index = channel.empty() + ch_reference_fasta_fai = channel.empty() + ch_reference_fasta = channel.empty() // // MODULE: Run Seqtk sample to perform subsampling // if (!("seqtk_sample" in skip_tools) && params.sample_size > 0) { ch_sample_sized = SEQTK_SAMPLE( - ch_samplesheet.map { - meta, reads -> [meta, reads, params.sample_size] + ch_samplesheet.map { meta, reads -> + [meta, reads, params.sample_size] } ).reads ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) - } else { + } + else { // No subsampling ch_sample_sized = ch_samplesheet } @@ -59,9 +70,9 @@ workflow SEQINSPECTOR { // MODULE: Run FastQC // if (!("fastqc" in skip_tools)) { - FASTQC ( - ch_sample_sized.map { - meta, subsampled -> [meta, subsampled] + FASTQC( + ch_sample_sized.map { meta, subsampled -> + [meta, subsampled] } ) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip) @@ -73,9 +84,8 @@ workflow SEQINSPECTOR { // Module: Run SeqFu stats // if (!("seqfu_stats" in skip_tools)) { - SEQFU_STATS ( - ch_samplesheet - .map { meta, reads -> + SEQFU_STATS( + ch_samplesheet.map { meta, reads -> [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads] } ) @@ -91,100 +101,170 @@ workflow SEQINSPECTOR { // and transpose it into a tuple containing lists for each property if (!("fastqscreen" in skip_tools)) { - ch_fastqscreen_refs = Channel - .fromList(samplesheetToList( - params.fastq_screen_references, - "${projectDir}/assets/schema_fastq_screen_references.json" - )) + ch_fastqscreen_refs = channel.fromList( + samplesheetToList( + params.fastq_screen_references, + "${projectDir}/assets/schema_fastq_screen_references.json", + ) + ) .toList() .transpose() .toList() - FASTQSCREEN_FASTQSCREEN ( + FASTQSCREEN_FASTQSCREEN( ch_samplesheet, - ch_fastqscreen_refs + ch_fastqscreen_refs, ) ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt) ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first()) } - // MODULE: Create BWA-MEM2 index of the reference genome - + // MODULE: Create BWA-MEM2 index of the reference genome OR use pre-built index if (!("bwamem2_index" in skip_tools)) { - ch_reference_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() + // Always create the reference FASTA channel since it's needed by BWAMEM2_MEM + ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() - BWAMEM2_INDEX ( - ch_reference_fasta - ) - ch_bwamem2_index = BWAMEM2_INDEX.out.index - ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions) + if (params.bwa_index) { + // Use pre-built index when --bwa_index parameter is provided + ch_bwamem2_index = channel.fromPath(params.bwa_index, checkIfExists: true) + .map { index_dir -> tuple([id: index_dir.name], index_dir) } + .collect() + // Add debug output to verify the pre-built index is being used + ch_bwamem2_index.view { "Using pre-built BWA-MEM2 index: ${it}" } + } + else { + // Build index from reference FASTA when no pre-built index is provided + BWAMEM2_INDEX( + ch_reference_fasta + ) + ch_bwamem2_index = BWAMEM2_INDEX.out.index + ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions) + + // Add debug output to verify the index was built + ch_bwamem2_index.view { "Built BWA-MEM2 index: ${it}" } + } } + // MODULE: Align reads with BWA-MEM2 if (!("bwamem2_mem" in skip_tools)) { - BWAMEM2_MEM ( + BWAMEM2_MEM( ch_sample_sized, ch_bwamem2_index, ch_reference_fasta, - params.sort_bam ?: true + params.sort_bam ?: true, ) ch_bwamem2_mem = BWAMEM2_MEM.out.bam ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions) - ch_bwamem2_mem.view { "BAM: $it" } + ch_bwamem2_mem.view { "BAM: ${it}" } + } + // MODULE: Index BAM files with Samtools + if (!("samtools_index" in skip_tools) && !("bwamem2_mem" in skip_tools)) { + SAMTOOLS_INDEX( + ch_bwamem2_mem + ) + ch_samtools_index = SAMTOOLS_INDEX.out.bai + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + ch_samtools_index.view { "BAI: ${it}" } + } + // MODULE: Index reference FASTA with Samtools faidx + if (!("samtools_faidx" in skip_tools)) { -} + // Assume ch_fasta emits tuple(meta, fasta) + ch_dummy_fai = channel.value(['dummy_meta', file('empty.fai')]) + + + SAMTOOLS_FAIDX( + ch_reference_fasta, + ch_dummy_fai, + true, + ) + ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + } + + // MODULE: Prepare BAM/BAI tuples for Picard + // Combine BAM and BAI outputs for Picard + if (!("picard_collectmultiplemetrics" in skip_tools) && !("bwamem2_mem" in skip_tools) && !("samtools_index" in skip_tools) && !("samtools_faidx" in skip_tools)) { + + // Prepare BAM/BAI tuples for Picard + ch_bam_bai = ch_bwamem2_mem + .join(ch_samtools_index) + .map { meta, bam, bai -> + [meta, bam, bai] + } + + ch_bam_bai.view { "Combined BAM/BAI for Picard: ${it}" } + ch_fasta = ch_reference_fasta + ch_fai = ch_reference_fasta_fai + + ch_fasta.view { "FASTA for Picard: ${it}" } + ch_fai.view { "FAI for Picard: ${it}" } + + PICARD_COLLECTMULTIPLEMETRICS( + ch_bam_bai, + ch_fasta, + ch_fai, + ) + + ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics) + ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first()) + } // Collate and save software versions // softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_' + 'seqinspector_software_' + 'mqc_' + 'versions.yml', + name: 'nf_core_' + 'seqinspector_software_' + 'mqc_' + 'versions.yml', sort: true, - newLine: true - ).set { ch_collated_versions } + newLine: true, + ) + .set { ch_collated_versions } // // MODULE: MultiQC // - ch_multiqc_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() - - summary_params = paramsSummaryMap( - workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value( - paramsSummaryMultiqc(summary_params)) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? - file(params.multiqc_methods_description, checkIfExists: true) : - file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value( - methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_config = params.multiqc_config + ? channel.fromPath(params.multiqc_config, checkIfExists: true) + : channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_logo = params.multiqc_logo + ? channel.fromPath(params.multiqc_logo, checkIfExists: true) + : channel.empty() + + summary_params = paramsSummaryMap( + workflow, + parameters_schema: "nextflow_schema.json" + ) + ch_workflow_summary = channel.value( + paramsSummaryMultiqc(summary_params) + ) + ch_multiqc_custom_methods_description = params.multiqc_methods_description + ? file(params.multiqc_methods_description, checkIfExists: true) + : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = channel.value( + methodsDescriptionText(ch_multiqc_custom_methods_description) + ) ch_multiqc_extra_files = ch_multiqc_extra_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml') + ) ch_multiqc_extra_files = ch_multiqc_extra_files.mix(ch_collated_versions) ch_multiqc_extra_files = ch_multiqc_extra_files.mix( ch_methods_description.collectFile( name: 'methods_description_mqc.yaml', - sort: true + sort: true, ) ) - MULTIQC_GLOBAL ( - ch_multiqc_files - .map { meta, file -> file } - .mix(ch_multiqc_extra_files) - .collect(), + MULTIQC_GLOBAL( + ch_multiqc_files.map { meta, file -> file }.mix(ch_multiqc_extra_files).collect(), ch_multiqc_config.toList(), [], ch_multiqc_logo.toList(), [], - [] + [], ) ch_tags = ch_multiqc_files @@ -192,8 +272,7 @@ workflow SEQINSPECTOR { .flatten() .unique() - multiqc_extra_files_per_tag = ch_tags - .combine(ch_multiqc_extra_files) + multiqc_extra_files_per_tag = ch_tags.combine(ch_multiqc_extra_files) // Group samples by tag tagged_mqc_files = ch_tags @@ -203,8 +282,7 @@ workflow SEQINSPECTOR { .mix(multiqc_extra_files_per_tag) .groupTuple() .tap { mqc_by_tag } - .collectFile { - sample_tag, _samples -> + .collectFile { sample_tag, _samples -> def prefix_tag = "[TAG:${sample_tag}]" [ "${prefix_tag}_multiqc_extra_config.yml", @@ -212,10 +290,10 @@ workflow SEQINSPECTOR { |output_fn_name: \"${prefix_tag}_multiqc_report.html\" |data_dir_name: \"${prefix_tag}_multiqc_data\" |plots_dir_name: \"${prefix_tag}_multiqc_plots\" - """.stripMargin() + """.stripMargin(), ] } - .map { file -> [ (file =~ /\[TAG:(.+)\]/)[0][1], file ] } + .map { file -> [(file =~ /\[TAG:(.+)\]/)[0][1], file] } .join(mqc_by_tag) .multiMap { _sample_tag, config, samples -> samples_per_tag: samples.flatten() @@ -228,17 +306,11 @@ workflow SEQINSPECTOR { tagged_mqc_files.config, ch_multiqc_logo.toList(), [], - [] + [], ) emit: - global_report = MULTIQC_GLOBAL.out.report.toList() // channel: [ /path/to/multiqc_report.html ] - grouped_reports = MULTIQC_PER_TAG.out.report.toList() // channel: [ /path/to/multiqc_report.html ] - versions = ch_versions // channel: [ path(versions.yml) ] + global_report = MULTIQC_GLOBAL.out.report.toList() // channel: [ /path/to/multiqc_report.html ] + grouped_reports = MULTIQC_PER_TAG.out.report.toList() // channel: [ /path/to/multiqc_report.html ] + versions = ch_versions // channel: [ path(versions.yml) ] } - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/