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Merge pull request #61 from MoTrPAC/chore/cleanup
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Major repo cleanup
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@mihirsamdarshi
mihirsamdarshi authored Mar 24, 2023
2 parents aff07a7 + 285f874 commit 11e6b5b
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Showing 29 changed files with 152 additions and 334 deletions.
12 changes: 6 additions & 6 deletions config/backends/gcp/google_prod_PAPI.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ engine {
filesystems {
gcs {
auth = "application-default"
project = "***REMOVED***"
project = "my-project"
}
}
}
Expand All @@ -28,12 +28,12 @@ backend {
actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
config {
// Google project
project = "***REMOVED***"
project = "my-project"

// Base bucket for workflow executions
# root="gs://***REMOVED***/PASS1A/Stanford/batch2/"
# root="gs://***REMOVED***/qctest/"
root="gs://***REMOVED***/PASS1A/mtsinai/batch3/checksum/"
# root="gs://my-bucket/PASS1A/Stanford/batch2/"
# root="gs://my-bucket/qctest/"
root="gs://my-bucket/PASS1A/mtsinai/batch3/checksum/"
// Polling for completion backs-off gradually for slower-running jobs.
// This is the maximum polling interval (in seconds):
maximum-polling-interval = 600
Expand Down Expand Up @@ -67,7 +67,7 @@ backend {
gcs {
// A reference to a potentially different auth for manipulating files via engine functions.
auth = "application-default"
project = "***REMOVED***"
project = "my-project"
}
}
}
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192 changes: 0 additions & 192 deletions docs/README_unpolished.md
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This file was deleted.

46 changes: 23 additions & 23 deletions examples/input_json/rat/rnaseq_pipeline_inputs_gcp.json
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Original file line number Diff line number Diff line change
@@ -1,95 +1,95 @@
{
"rnaseq_pipeline.fastq1": [
"gs://my-bucket/rna-seq/test_data/8019468198_R1.fastq.gz"
"gs://mihir-test/rna-seq/test_data/8019468198_R1.fastq.gz"
],
"rnaseq_pipeline.fastq2": [
"gs://my-bucket/rna-seq/test_data/8019468198_R2.fastq.gz"
"gs://mihir-test/rna-seq/test_data/8019468198_R2.fastq.gz"
],
"rnaseq_pipeline.fastq_index": [
"gs://my-bucket/rna-seq/test_data/8019468198_I1.fastq.gz"
"gs://mihir-test/rna-seq/test_data/8019468198_I1.fastq.gz"
],
"rnaseq_pipeline.sample_prefix": [
"8019468198"
],
"rnaseq_pipeline.pretrim_fastqc_ncpu": 8,
"rnaseq_pipeline.pretrim_fastqc_ramGB": 40,
"rnaseq_pipeline.pretrim_fastqc_disk": 100,
"rnaseq_pipeline.fastqc_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/fastqc:latest",
"rnaseq_pipeline.fastqc_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/fastqc:latest",
"rnaseq_pipeline.attach_umi_ncpu": 8,
"rnaseq_pipeline.attach_umi_ramGB": 40,
"rnaseq_pipeline.attach_umi_disk": 100,
"rnaseq_pipeline.attach_umi_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/umi_attach:latest",
"rnaseq_pipeline.attach_umi_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/umi_attach:latest",
"rnaseq_pipeline.minimumLength": 20,
"rnaseq_pipeline.index_adapter": "AGATCGGAAGAGC",
"rnaseq_pipeline.univ_adapter": "AGATCGGAAGAGC",
"rnaseq_pipeline.cutadapt_ncpu": 8,
"rnaseq_pipeline.cutadapt_ramGB": 45,
"rnaseq_pipeline.cutadapt_disk": 100,
"rnaseq_pipeline.cutadapt_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/cutadapt:latest",
"rnaseq_pipeline.cutadapt_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/cutadapt:latest",
"rnaseq_pipeline.posttrim_fastqc_ncpu": 8,
"rnaseq_pipeline.posttrim_fastqc_ramGB": 36,
"rnaseq_pipeline.posttrim_fastqc_disk": 100,
"rnaseq_pipeline.multiqc_ncpu": 8,
"rnaseq_pipeline.multiqc_ramGB": 20,
"rnaseq_pipeline.multiqc_disk": 100,
"rnaseq_pipeline.multiqc_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/multiqc:latest",
"rnaseq_pipeline.star_index": "gs://my-bucket/references/rn/v96/star_2.7.0d_04-20-19/Rnor6_v96_star_index.tar.gz",
"rnaseq_pipeline.multiqc_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/multiqc:latest",
"rnaseq_pipeline.star_index": "gs://mihir-test/references/rn/v96/star_2.7.0d_04-20-19/Rnor6_v96_star_index.tar.gz",
"rnaseq_pipeline.star_ncpu": 10,
"rnaseq_pipeline.star_ramGB": 96,
"rnaseq_pipeline.star_disk": 200,
"rnaseq_pipeline.star_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/star:latest",
"rnaseq_pipeline.gtf_file": "gs://my-bucket/references/rn/v96/Rattus_norvegicus.Rnor_6.0.96.gtf",
"rnaseq_pipeline.star_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/star:latest",
"rnaseq_pipeline.gtf_file": "gs://mihir-test/references/rn/v96/Rattus_norvegicus.Rnor_6.0.96.gtf",
"rnaseq_pipeline.feature_counts_ncpu": 8,
"rnaseq_pipeline.feature_counts_ramGB": 48,
"rnaseq_pipeline.feature_counts_disk": 100,
"rnaseq_pipeline.feature_counts_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/feature_counts:latest",
"rnaseq_pipeline.rsem_reference": "gs://my-bucket/references/rn/v96/rsem/rn6_rsem_reference.tar.gz",
"rnaseq_pipeline.feature_counts_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/feature_counts:latest",
"rnaseq_pipeline.rsem_reference": "gs://mihir-test/references/rn/v96/rsem/rn6_rsem_reference.tar.gz",
"rnaseq_pipeline.rsem_ncpu": 10,
"rnaseq_pipeline.rsem_ramGB": 48,
"rnaseq_pipeline.rsem_disk": 150,
"rnaseq_pipeline.rsem_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/rsem:latest",
"rnaseq_pipeline.rsem_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/rsem:latest",
"rnaseq_pipeline.globin_genome_dir": "rn_globin",
"rnaseq_pipeline.globin_genome_dir_tar": "gs://my-bucket/references/rn/bowtie2_index/rn_globin.tar.gz",
"rnaseq_pipeline.globin_genome_dir_tar": "gs://mihir-test/references/rn/bowtie2_index/rn_globin.tar.gz",
"rnaseq_pipeline.bowtie2_globin_ncpu": 12,
"rnaseq_pipeline.bowtie2_globin_ramGB": 80,
"rnaseq_pipeline.bowtie2_globin_disk": 200,
"rnaseq_pipeline.rrna_genome_dir": "rn_rRNA",
"rnaseq_pipeline.rrna_genome_dir_tar": "gs://my-bucket/references/rn/bowtie2_index/rn_rRNA.tar.gz",
"rnaseq_pipeline.rrna_genome_dir_tar": "gs://mihir-test/references/rn/bowtie2_index/rn_rRNA.tar.gz",
"rnaseq_pipeline.bowtie2_rrna_ncpu": 12,
"rnaseq_pipeline.bowtie2_rrna_ramGB": 80,
"rnaseq_pipeline.bowtie2_rrna_disk": 200,
"rnaseq_pipeline.phix_genome_dir": "phix",
"rnaseq_pipeline.phix_genome_dir_tar": "gs://my-bucket/references/rn/bowtie2_index/phix.tar.gz",
"rnaseq_pipeline.phix_genome_dir_tar": "gs://mihir-test/references/rn/bowtie2_index/phix.tar.gz",
"rnaseq_pipeline.bowtie2_phix_ncpu": 12,
"rnaseq_pipeline.bowtie2_phix_ramGB": 80,
"rnaseq_pipeline.bowtie2_phix_disk": 200,
"rnaseq_pipeline.bowtie_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/bowtie:latest",
"rnaseq_pipeline.bowtie_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/bowtie:latest",
"rnaseq_pipeline.markdup_ncpu": 10,
"rnaseq_pipeline.markdup_ramGB": 48,
"rnaseq_pipeline.markdup_disk": 150,
"rnaseq_pipeline.ref_flat": "gs://my-bucket/references/rn/v96/refFlat_rn6_v96.txt",
"rnaseq_pipeline.ref_flat": "gs://mihir-test/references/rn/v96/refFlat_rn6_v96.txt",
"rnaseq_pipeline.rnaqc_ncpu": 10,
"rnaseq_pipeline.rnaqc_ramGB": 48,
"rnaseq_pipeline.rnaqc_disk": 100,
"rnaseq_pipeline.picard_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/picard:latest",
"rnaseq_pipeline.picard_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/picard:latest",
"rnaseq_pipeline.umi_dup_ncpu": 8,
"rnaseq_pipeline.umi_dup_ramGB": 36,
"rnaseq_pipeline.umi_dup_disk": 200,
"rnaseq_pipeline.umi_dup_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/umi_dup:latest",
"rnaseq_pipeline.umi_dup_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/umi_dup:latest",
"rnaseq_pipeline.mapped_ncpu": 8,
"rnaseq_pipeline.mapped_ramGB": 36,
"rnaseq_pipeline.mapped_disk": 200,
"rnaseq_pipeline.samtools_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/samtools:latest",
"rnaseq_pipeline.samtools_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/samtools:latest",
"rnaseq_pipeline.mqc_postalign_ncpu": 8,
"rnaseq_pipeline.mqc_postalign_ramGB": 36,
"rnaseq_pipeline.mqc_postalign_disk": 50,
"rnaseq_pipeline.collect_qc_ncpu": 8,
"rnaseq_pipeline.collect_qc_ramGB": 16,
"rnaseq_pipeline.collect_qc_disk": 50,
"rnaseq_pipeline.collect_qc_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/collect_qc:latest",
"rnaseq_pipeline.collect_qc_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/collect_qc:latest",
"rnaseq_pipeline.output_report_name": "ms_pipeline_test",
"rnaseq_pipeline.merge_results_ncpu": 4,
"rnaseq_pipeline.merge_results_ramGB": 16,
"rnaseq_pipeline.merge_results_disk": 10,
"rnaseq_pipeline.merge_results_docker": "gcr.io/***REMOVED***-dev/motrpac-rna-seq-pipeline/merge_results:latest"
"rnaseq_pipeline.merge_results_docker": "gcr.io/motrpac-portal-dev/motrpac-rna-seq-pipeline/merge_results:latest"
}
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