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parameters.settings.json
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parameters.settings.json
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{
"parameters": [
{
"name": "reads",
"label": "Input files",
"usage": "Specify the location of your input FastQ files.",
"group": "Main options",
"default_value": "'data/*{1,2}.fastq.gz'",
"render": "textfield",
"pattern": ".*\\*.*",
"type": "string"
},
{
"name": "outdir",
"label": "Output directory",
"usage": "Set where to save the results from the pipeline",
"group": "Main options",
"default_value": "./results",
"render": "textfield",
"pattern": ".*",
"type": "string"
},
{
"name": "rrbs",
"label": "Library type: rrbs",
"usage": "Set trimming settings for MspI digested samples",
"group": "Trimming presets",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "pbat",
"label": "Library type: pbat",
"usage": "Set trimming settings for post-bisulfite adapter tagging (PBAT).",
"group": "Trimming presets",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "single_cell",
"label": "Library type: Single cell",
"usage": "Set trimming settings for Single Cell libraries",
"group": "Trimming presets",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "epignome",
"label": "Library type: TruSeq (EpiGnome)",
"usage": "Set trimming settings for TruSeq (EpiGnome) libraries",
"group": "Trimming presets",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "accel",
"label": "Library type: Accel-NGS (Swift)",
"usage": "Set trimming settings for Accel-NGS (Swift) libraries",
"group": "Trimming presets",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "zymo",
"label": "Library type: Zymo Pico-Methyl",
"usage": "Set trimming settings for Zymo Pico-Methyl libraries",
"group": "Trimming presets",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "cegx",
"label": "Library type: CEGX",
"usage": "Set trimming settings for CEGX libraries",
"group": "Trimming presets",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "single_end",
"label": "Single-end sequencing input",
"usage": "Use single-end sequencing inputs instead of paired-end.",
"group": "Main options",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "clip_r1",
"label": "Read Clipping: 5' R1",
"usage": "Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).",
"group": "Read trimming",
"render": "textfield",
"pattern": "\\d*",
"type": "integer",
"default_value": 0
},
{
"name": "clip_r2",
"label": "Read Clipping: 5' R1",
"usage": "Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).",
"group": "Read trimming",
"render": "textfield",
"pattern": "\\d*",
"type": "integer",
"default_value": 0
},
{
"name": "three_prime_clip_r1",
"label": "Read Clipping: 3' R1",
"usage": "Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.",
"group": "Read trimming",
"render": "textfield",
"pattern": "\\d*",
"type": "integer",
"default_value": 0
},
{
"name": "three_prime_clip_r2",
"label": "Read Clipping: 3' R2",
"usage": "Instructs Trim Galore to re move bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.",
"group": "Read trimming",
"render": "textfield",
"pattern": "\\d*",
"type": "integer",
"default_value": 0
},
{
"name": "aligner",
"label": "Alignment tool",
"usage": "Choose whether to align reads with bismark (Bowtie2), bismark_hisat (HISAT2) or bwameth (BWA)",
"type": "string",
"render": "radio-button",
"choices": [
"bismark",
"bismark_hisat",
"bwameth"
],
"default_value": "bismark",
"group": "Alignment"
},
{
"name": "genome",
"label": "Alignment reference iGenomes key",
"usage": "Ref. genome key for iGenomes",
"group": "Alignment",
"render": "drop-down",
"type": "string",
"choices": [
"",
"GRCh38",
"GRCh37",
"GRCm38",
"TAIR10",
"EB2",
"UMD3.1",
"WBcel235",
"CanFam3.1",
"GRCz10",
"BDGP6",
"EquCab2",
"EB1",
"Galgal4",
"Gm01",
"Mmul_1",
"IRGSP-1.0",
"CHIMP2.1.4",
"Rnor_6.0",
"R64-1-1",
"EF2",
"Sbi1",
"Sscrofa10.2",
"AGPv3"
],
"default_value": ""
},
{
"name": "bismark_index",
"label": "bismark index",
"usage": "Path to bismark index (either Bowtie2 or HISAT2, depending on aligner option)",
"group": "Alignment",
"render": "file",
"type": "string",
"pattern": ".*",
"default_value": ""
},
{
"name": "bwa_meth_index",
"label": "bwameth index",
"usage": "Path to bwameth index",
"group": "Alignment",
"render": "file",
"type": "string",
"pattern": ".*",
"default_value": ""
},
{
"name": "fasta_index",
"label": "fasta index",
"usage": "Path to fasta index",
"group": "Alignment",
"render": "file",
"type": "string",
"pattern": ".*",
"default_value": ""
},
{
"name": "fasta",
"label": "FASTA",
"usage": "Path to Fasta reference",
"group": "Alignment",
"render": "file",
"type": "string",
"pattern": ".*",
"default_value": ""
},
{
"name": "known_splices",
"label": "GTF",
"usage": "Path to GTF file (bismark_hisat only)",
"group": "Advanced: bismark_hisat workflow only",
"render": "file",
"type": "string",
"pattern": ".*",
"default_value": false
},
{
"name": "igenomes_base",
"label": "iGenomes base path",
"usage": "Base path for iGenomes reference files",
"group": "Alignment",
"default_value": "s3://ngi-igenomes/igenomes/",
"render": "textfield",
"pattern": ".*",
"type": "string"
},
{
"name": "container",
"label": "Software container",
"usage": "Dockerhub address for pipeline container",
"default_value": "nfcore/methylseq:latest",
"render": "textfield",
"pattern": ".*",
"type": "string",
"group": "Pipeline defaults"
},
{
"name": "plaintext_email",
"label": "Plain text email",
"usage": "Set to receive plain-text e-mails instead of HTML formatted.",
"group": "Pipeline defaults",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "help",
"label": "Help",
"usage": "Specify to show the pipeline help text.",
"group": "Pipeline defaults",
"render": "none",
"default_value": false,
"type": "boolean"
},
{
"name": "email",
"label": "Your email address",
"usage": "Your email address, required to receive completion notification.",
"group": "Pipeline defaults",
"render": "textfield",
"pattern": "^$|(^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\\.[a-zA-Z0-9-.]+$)",
"type": "string",
"default_value": ""
},
{
"name": "max_cpus",
"label": "Maximum available CPUs",
"usage": "Use to set a top-limit for the default CPUs requirement for each process.",
"group": "Pipeline defaults",
"default_value": 16,
"render": "textfield",
"type": "integer"
},
{
"name": "max_time",
"label": "Maximum available time",
"usage": "Use to set a top-limit for the default time requirement for each process.",
"group": "Pipeline defaults",
"default_value": "10d",
"render": "textfield",
"pattern": "\\d+[smhd]",
"type": "string"
},
{
"name": "max_memory",
"label": "Maximum available memory",
"usage": "Use to set a top-limit for the default memory requirement for each process.",
"group": "Pipeline defaults",
"default_value": "128.GB",
"render": "textfield",
"pattern": "\\d+\\.[KMGT]?B",
"type": "string"
},
{
"name": "save_trimmed",
"label": "Save Trimmed FastQ files",
"usage": "Save the trimmed FastQ files the the results directory.",
"group": "Pipeline defaults",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "save_align_intermeds",
"label": "Save Aligned Intermediate BAM files",
"usage": "Save intermediate BAM files the the results directory.",
"group": "Pipeline defaults",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "save_reference",
"label": "Save reference genome index",
"usage": "Save the generated reference files the the results directory.",
"group": "Pipeline defaults",
"render": "check-box",
"default_value": false,
"type": "boolean"
},
{
"name": "max_multiqc_email_size",
"label": "Maximum MultiQC email file size",
"usage": "Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached.",
"group": "Pipeline defaults",
"default_value": "25.MB",
"render": "textfield",
"pattern": "\\d+\\.[KMGT]?B",
"type": "string"
},
{
"name": "skip_deduplication",
"label": "Skip deduplication step after alignment (turned on automatically if --rrbs is set)",
"render": "check-box",
"default_value": false,
"type": "boolean",
"group": "Skip pipeline steps"
},
{
"name": "skip_trimming",
"label": "Skip read trimming",
"render": "check-box",
"default_value": false,
"type": "boolean",
"group": "Skip pipeline steps"
},
{
"name": "project",
"label": "Cluster project",
"usage": "For use on HPC systems where a project ID is required for job submission",
"group": "Cluster job submission",
"render": "textfield",
"pattern": ".*",
"type": "string",
"default_value": ""
},
{
"name": "awsregion",
"label": "AWS Region",
"usage": "The AWS region to run your job in.",
"group": "AWS cloud usage",
"default_value": "eu-west-1",
"render": "textfield",
"pattern": ".*",
"type": "string"
},
{
"name": "awsqueue",
"label": "AWS job queue",
"usage": "The JobQueue that you intend to use on AWS Batch.",
"group": "AWS cloud usage",
"render": "textfield",
"pattern": ".*",
"type": "string",
"default_value": ""
},
{
"name": "tracedir",
"label": "Trace directory",
"usage": "Set to where the pipeline trace should be saved. Set to local path when using AWS on S3.",
"group": "AWS cloud usage",
"default_value": "./results/pipeline_info",
"render": "textfield",
"pattern": ".*",
"type": "string"
},
{
"name": "subsampFilesizeThreshold",
"label": "Subsample file-size threshold",
"usage": "Defines the threshold in BAM file size (in bytes) at which data subsampling is used prior to the RSeQC `gene_body_coverage` step.",
"group": "Advanced",
"default_value": 10000000000,
"render": "textfield",
"pattern": "\\d*",
"type": "integer"
},
{
"name": "name",
"label": "Custom run name",
"usage": "Helper variable. Do not set, use -name instead.",
"group": "Advanced",
"render": "none",
"pattern": ".*",
"type": "string",
"default_value": ""
},
{
"name": "hisatBuildMemory",
"label": "HISAT2 indexing: required memory for splice sites in GB",
"usage": "HISAT2 needs a very large amount of memory to build an index with splice sites. If the available memory is below this threshold, the index build will proceed without splicing information.",
"group": "Advanced",
"default_value": 200,
"render": "textfield",
"type": "integer"
},
{
"name": "multiqc_config",
"label": "MultiQC Config",
"usage": "Path to a config file for MultiQC",
"group": "Advanced",
"default_value": "assets/multiqc_config.yaml",
"render": "file",
"pattern": ".*\\.yaml",
"type": "string"
},
{
"name": "unmapped",
"label": "Unmapped",
"usage": "Save unmapped reads to fastq files",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bismark workflow only"
},
{
"name": "non_directional",
"label": "Non-directional",
"usage": "Run alignment against all four possible strands",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bismark workflow only"
},
{
"name": "ignore_flags",
"label": "Ignore SAM flags",
"usage": "Run MethylDackel with the flag to ignore SAM flags",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bwameth workflow only"
},
{
"name": "comprehensive",
"label": "Comprehensive output",
"usage": "Output information for all cytosine contexts",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bismark workflow only"
},
{
"name": "meth_cutoff",
"label": "Methylation cutoff",
"usage": "Specify a minimum read coverage to report a methylation call during Bismark's bismark_methylation_extractor step.",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bismark workflow only"
},
{
"name": "min_depth",
"label": "Methylation cutoff",
"usage": "Specify a minimum read coverage for MethylDackel to report a methylation call.",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bwameth workflow only"
},
{
"name": "methyl_kit",
"label": "methylKit output",
"usage": "Run MethylDackel with the --methylKit flag to produce files suitable for use with the methylKit R package.",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bwameth workflow only"
},
{
"name": "slamseq",
"label": "SLAM-seq mode",
"usage": "Run bismark in SLAM-seq mode",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bismark_hisat workflow only"
},
{
"name": "local_alignment",
"label": "Soft-clipping of reads",
"usage": "Run bismark with --local flag to allow soft-clipping of reads (potentially useful for single-cell experiments)",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bismark workflow only"
},
{
"name": "relax_mismatches",
"label": "Relax mismatches",
"usage": "Turn on to relax stringency for alignment (set allowed penalty with --num_mismatches)",
"render": "none",
"default_value": false,
"type": "boolean",
"group": "Advanced: bismark workflow only"
},
{
"name": "num_mismatches",
"label": "Mismatch penalty",
"usage": "0.6 will allow a penalty of bp * -0.6 - for 100bp reads (bismark default is 0.2)",
"render": "none",
"default_value": 0.6,
"type": "decimal",
"group": "Advanced: bismark workflow only"
},
{
"name": "readPaths",
"label": "Read Paths",
"usage": "For use with nextflow config files only",
"group": "Advanced",
"render": "none",
"pattern": ".*",
"type": "string",
"default_value": ""
}
]
}