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PathogenWorkflows_cwl.json
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PathogenWorkflows_cwl.json
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{
"sbg:revision": 1,
"steps": [
{
"run": {
"temporaryFailCodes": [],
"baseCommand": [
"tar",
"-xvf",
{
"script": "$job.inputs.genome.path",
"class": "Expression",
"engine": "#cwl-js-engine"
},
"&&",
"/opt/STAR-2.5.1b/bin/Linux_x86_64_static/STAR",
"--runThreadN",
{
"script": "{\n return $job.allocatedResources.cpu\n}",
"class": "Expression",
"engine": "#cwl-js-engine"
}
],
"sbg:revision": 0,
"successCodes": [],
"y": 196.68230040930223,
"sbg:job": {
"inputs": {
"unmappedOutputName": "Uncontamimated",
"chimJunctionOverhangMin": 0,
"alignEndsType": "Local",
"scoreDelOpen": 0,
"seedSearchStartLmax": 0,
"rg_platform_unit_id": "rg_platform_unit",
"outSJfilterIntronMaxVsReadN": [
0
],
"sjdbScore": null,
"chimScoreJunctionNonGTAG": 0,
"alignSoftClipAtReferenceEnds": "Yes",
"alignSplicedMateMapLminOverLmate": 0,
"outSAMheaderHD": "outSAMheaderHD",
"chimSegmentMin": 15,
"seedSearchStartLmaxOverLread": 0,
"outSJfilterOverhangMin": [
30,
12,
12,
12
],
"outSJfilterCountTotalMin": [
3,
1,
1,
1
],
"outSAMmode": "Full",
"winFlankNbins": 0,
"rg_sample_id": "rg_sample",
"outSAMunmapped": "None",
"chimScoreSeparation": 0,
"scoreStitchSJshift": 0,
"winAnchorDistNbins": 0,
"twopassMode": "Basic",
"outSAMfilter": "KeepOnlyAddedReference",
"outFilterScoreMinOverLread": 0,
"scoreGapGCAG": 0,
"alignSJDBoverhangMin": 0,
"outSAMprimaryFlag": "OneBestScore",
"reads": [
{
"metadata": {
"paired_end": "1"
},
"class": "File",
"path": "/test-data/test_sample_1.fastq",
"secondaryFiles": [],
"size": 0
}
],
"sortUnmappedReads": true,
"clip3pAdapterMMp": [
0
],
"limitOutSJcollapsed": 0,
"outFilterType": "Normal",
"winAnchorMultimapNmax": 0,
"seedSearchLmax": 0,
"readMapNumber": 0,
"alignIntronMax": 0,
"limitOutSJoneRead": 0,
"outFilterMismatchNoverReadLmax": 0,
"chimFilter": "banGenomicN",
"scoreGenomicLengthLog2scale": 0,
"seedMultimapNmax": 0,
"scoreInsBase": 0,
"sjdbGTFchrPrefix": "chrPrefix",
"sjdbOverhang": null,
"outFilterMultimapScoreRange": 0,
"outSJfilterCountUniqueMin": [
3,
1,
1,
1
],
"chimOutType": "Within",
"alignWindowsPerReadNmax": 0,
"sjdbInsertSave": "Basic",
"genome": {
"class": "File",
"path": "genome.ext",
"secondaryFiles": [],
"size": 0
},
"alignSplicedMateMapLmin": 0,
"outFilterMultimapNmax": 0,
"outReadsUnmapped": "Fastx",
"outSAMstrandField": "None",
"scoreGapNoncan": 0,
"quantTranscriptomeBan": "IndelSoftclipSingleend",
"alignSJstitchMismatchNmax": "alignSJstitchMismatchNmax-string-value",
"scoreGapATAC": 0,
"outSAMmultNmax": 0,
"quantMode": "TranscriptomeSAM",
"outSJfilterDistToOtherSJmin": [
0
],
"winBinNbits": 0,
"sjdbGTFfile": [
{
"path": "/demo/test-data/chr20.gtf"
}
],
"alignTranscriptsPerReadNmax": 0,
"outFilterMatchNminOverLread": 0,
"limitBAMsortRAM": 0,
"outSAMflagOR": 0,
"limitSjdbInsertNsj": 0,
"scoreInsOpen": 0,
"outSJfilterReads": "All",
"seedPerReadNmax": 0,
"sjdbGTFtagExonParentGene": "",
"clip5pNbases": [
0
],
"outSAMheaderPG": "outSAMheaderPG",
"twopass1readsN": -2,
"outMultimapperOrder": "Random",
"outSAMtype": "SAM",
"outFilterMismatchNmax": 0,
"outSAMreadID": "Standard",
"outSAMflagAND": 0,
"outSAMattributes": "Standard",
"scoreDelBase": 0,
"clip3pNbases": [
0,
3
],
"outFilterScoreMin": 0,
"chimSegmentReadGapMax": 8,
"scoreGap": 0,
"outFilterMatchNmin": 0,
"outFilterIntronMotifs": "None",
"rg_seq_center": "",
"rg_library_id": "",
"alignIntronMin": 0,
"outSortingType": "SortedByCoordinate",
"outSAMmapqUnique": 0,
"GENOME_DIR_NAME": "",
"sjdbGTFfeatureExon": "",
"clip3pAfterAdapterNbases": [
0
],
"outFilterMismatchNoverLmax": 0,
"readMatesLengthsIn": "NotEqual",
"seedPerWindowNmax": 0,
"no_read_groups": false,
"rg_platform": "Ion Torrent PGM",
"clip3pAdapterSeq": [
"clip3pAdapterSeq"
],
"alignTranscriptsPerWindowNmax": 0,
"rg_mfl": "rg_mfl",
"chimScoreDropMax": 0,
"chimScoreMin": 0,
"alignSJoverhangMin": 0,
"outSAMorder": "Paired",
"seedNoneLociPerWindow": 0,
"outQSconversionAdd": 0,
"alignMatesGapMax": 0,
"outSAMattrIHstart": 6,
"sjdbGTFtagExonParentTranscript": ""
},
"allocatedResources": {
"mem": 60000,
"cpu": 32
}
},
"sbg:id": "krishnanus/initialtesting/star-2-5-1-b/0",
"sbg:validationErrors": [],
"sbg:toolkitVersion": "2.5.1b",
"sbg:categories": [
"Alignment"
],
"sbg:project": "krishnanus/initialtesting",
"sbg:copyOf": "admin/sbg-public-data/star-2-5-1-b/41",
"appUrl": "/u/krishnanus/initialtesting/apps/#krishnanus/initialtesting/star-2-5-1-b/0",
"x": 719.3333605925246,
"sbg:createdBy": "tsang",
"description": "STAR is an ultrafast universal RNA-seq aligner. It has very high mapping speed, accurate alignment of contiguous and spliced reads, detection of polyA-tails, non-canonical splices and chimeric (fusion) junctions. It works with reads starting from lengths ~15 bases up to ~300 bases. In case of having longer reads, use of STAR Long is recommended.\n\n###Common issues###\n1. In case of paired-end alignment it is crucial to set metadata 'paired-end' field to 1/2.\n2. Files in multi-FASTQ format are currently not supported, i.e. if you have single-end reads that span multiple FASTQ files, or paired-end reads that span more than 2 files, please use a tool like SBG Merge FASTQs before providing your files to the STAR aligner. \n3. If you are providing a GFF3 file and wish to use STAR results for further downstream analysis, a good idea would be to set the \"Exons' parents name\" (id: sjdbGTFtagExonParentTranscript) option to \"Parent\".\n4. Unmapped reads are, by default, unsorted. If you want to sort them by read ID, please specify the \"Sort unmapped reads\" option, though keep in mind that this can increase STAR run time.",
"sbg:links": [
{
"id": "https://github.com/alexdobin/STAR",
"label": "Homepage"
},
{
"id": "https://github.com/alexdobin/STAR/releases",
"label": "Releases"
},
{
"id": "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf",
"label": "Manual"
},
{
"id": "https://groups.google.com/forum/#!forum/rna-star",
"label": "Support"
},
{
"id": "http://www.ncbi.nlm.nih.gov/pubmed/23104886",
"label": "Publication"
}
],
"sbg:modifiedBy": "tsang",
"sbg:projectName": "InitialTesting",
"sbg:sbgMaintained": false,
"sbg:license": "GNU General Public License v3.0 only",
"label": "STAR",
"sbg:cmdPreview": "tar -xvf genome.ext && /opt/STAR-2.5.1b/bin/Linux_x86_64_static/STAR --runThreadN 32 --sjdbGTFfile /demo/test-data/chr20.gtf --sjdbGTFchrPrefix chrPrefix --sjdbInsertSave Basic --twopass1readsN -2 --chimOutType WithinSAM --outSAMattrRGline ID:1 PI:rg_mfl PL:Ion_Torrent_PGM PU:rg_platform_unit SM:rg_sample --quantMode TranscriptomeSAM --outFileNamePrefix ./test_sample_1.fastq. --readFilesIn /test-data/test_sample_1.fastq && tar -vcf test_sample_1.fastq._STARgenome.tar ./test_sample_1.fastq._STARgenome && cat test_sample_1.fastq.Unmapped.out.mate1 | sed 's/\\t.*//' | paste - - - - | sort -k1,1 -S 10G | tr '\\t' '\\n' > test_sample_1.fastq.Uncontamimated.mate1.fastq && rm test_sample_1.fastq.Unmapped.out.mate1",
"stdout": "",
"sbg:latestRevision": 0,
"hints": [
{
"dockerPull": "images.sbgenomics.com/ana_d/star-fusion:2.5.1b",
"class": "DockerRequirement",
"dockerImageId": ""
},
{
"class": "sbg:MemRequirement",
"value": 60000
},
{
"class": "sbg:CPURequirement",
"value": 32
}
],
"requirements": [
{
"id": "#cwl-js-engine",
"requirements": [
{
"dockerPull": "rabix/js-engine",
"class": "DockerRequirement"
}
],
"class": "ExpressionEngineRequirement"
}
],
"cwlVersion": "sbg:draft-2",
"sbg:appVersion": [
"sbg:draft-2"
],
"sbg:image_url": null,
"class": "CommandLineTool",
"sbg:createdOn": 1499349815,
"inputs": [
{
"sbg:toolDefaultValue": "4",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--winFlankNbins"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#winFlankNbins",
"label": "Flanking regions size",
"description": "=log2(winFlank), where win Flank is the size of the left and right flanking regions for each window (int>0).",
"sbg:category": "Windows, Anchors, Binning"
},
{
"sbg:toolDefaultValue": "16",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--winBinNbits"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#winBinNbits",
"label": "Bin size",
"description": "=log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins (int>0).",
"sbg:category": "Windows, Anchors, Binning"
},
{
"sbg:toolDefaultValue": "50",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--winAnchorMultimapNmax"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#winAnchorMultimapNmax",
"label": "Max loci anchors",
"description": "Max number of loci anchors are allowed to map to (int>0).",
"sbg:category": "Windows, Anchors, Binning"
},
{
"sbg:toolDefaultValue": "9",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--winAnchorDistNbins"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#winAnchorDistNbins",
"label": "Max bins between anchors",
"description": "Max number of bins between two anchors that allows aggregation of anchors into one window (int>0).",
"sbg:category": "Windows, Anchors, Binning"
},
{
"sbg:toolDefaultValue": "\"Unmapped.out\"",
"type": [
"null",
"string"
],
"required": false,
"id": "#unmappedOutputName",
"sbg:category": "Output",
"label": "Unmapped output file names",
"description": "Names of the unmapped output files.",
"sbg:includeInPorts": false
},
{
"sbg:toolDefaultValue": "None",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--twopassMode"
},
"type": [
"null",
{
"symbols": [
"None",
"Basic"
],
"name": "twopassMode",
"type": "enum"
}
],
"required": false,
"id": "#twopassMode",
"label": "Two-pass mode",
"description": "2-pass mapping mode. None: 1-pass mapping; Basic: basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly.",
"sbg:category": "2-pass mapping"
},
{
"sbg:toolDefaultValue": "-1",
"type": [
"null",
"int"
],
"required": false,
"id": "#twopass1readsN",
"label": "Reads to process in 1st step",
"description": "Number of reads to process for the 1st step. 0: 1-step only, no 2nd pass; use very large number (or default -1) to map all reads in the first step (int>0).",
"sbg:category": "2-pass mapping"
},
{
"sbg:toolDefaultValue": "Off",
"type": [
"null",
"boolean"
],
"required": false,
"id": "#sortUnmappedReads",
"label": "Sort unmapped reads",
"description": "Unmapped reads are, by default, unsorted. If you want to sort them by read ID, please specify this option, though keep in mind that this can increase STAR run time.",
"sbg:category": "Output"
},
{
"sbg:toolDefaultValue": "2",
"type": [
"null",
"int"
],
"required": false,
"id": "#sjdbScore",
"label": "Extra alignment score",
"description": "Extra alignment score for alignments that cross database junctions.",
"sbg:category": "Splice junctions database"
},
{
"sbg:toolDefaultValue": "100",
"type": [
"null",
"int"
],
"required": false,
"id": "#sjdbOverhang",
"label": "\"Overhang\" length",
"description": "Length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1) (int >= 0), if int = 0, splice junction database is not used.",
"sbg:category": "Splice junctions database"
},
{
"sbg:toolDefaultValue": "None",
"type": [
"null",
{
"symbols": [
"Basic",
"All",
"None"
],
"name": "sjdbInsertSave",
"type": "enum"
}
],
"required": false,
"id": "#sjdbInsertSave",
"label": "Save junction files",
"description": "Which files to save when sjdb junctions are inserted on the fly at the mapping step. None: not saving files at all; Basic: only small junction/transcript files; All: all files including big Genome, SA and SAindex. These files are output as archive.",
"sbg:category": "Splice junctions database"
},
{
"sbg:toolDefaultValue": "transcript_id",
"type": [
"null",
"string"
],
"required": false,
"id": "#sjdbGTFtagExonParentTranscript",
"label": "Exons' parents name",
"description": "Tag name to be used as exons transcript-parents.",
"sbg:category": "Splice junctions database"
},
{
"sbg:toolDefaultValue": "gene_id",
"type": [
"null",
"string"
],
"required": false,
"id": "#sjdbGTFtagExonParentGene",
"label": "Gene name",
"description": "Tag name to be used as exons gene-parents.",
"sbg:category": "Splice junctions database"
},
{
"sbg:fileTypes": "GTF, GFF, GFF2, GFF3, TXT",
"type": [
"null",
{
"name": "sjdbGTFfile",
"items": "File",
"type": "array"
}
],
"required": false,
"id": "#sjdbGTFfile",
"label": "Splice junction file",
"description": "Gene model annotations and/or known transcripts. No need to include this input, except in case of using \"on the fly\" annotations. If you are providing a GFF3 file and wish to use STAR results for further downstream analysis, a good idea would be to set the \"Exons' parents name\" (id: sjdbGTFtagExonParentTranscript) option to \"Parent\".",
"sbg:category": "Basic"
},
{
"sbg:toolDefaultValue": "exon",
"type": [
"null",
"string"
],
"required": false,
"id": "#sjdbGTFfeatureExon",
"label": "Set exons feature",
"description": "Feature type in GTF file to be used as exons for building transcripts.",
"sbg:category": "Splice junctions database"
},
{
"sbg:toolDefaultValue": "-",
"type": [
"null",
"string"
],
"required": false,
"id": "#sjdbGTFchrPrefix",
"label": "Chromosome names",
"description": "Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC geneomes).",
"sbg:category": "Splice junctions database"
},
{
"sbg:toolDefaultValue": "1.0",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--seedSearchStartLmaxOverLread"
},
"type": [
"null",
"float"
],
"required": false,
"id": "#seedSearchStartLmaxOverLread",
"label": "Search start point normalized",
"description": "SeedSearchStartLmax normalized to read length (sum of mates' lengths for paired-end reads).",
"sbg:category": "Alignments and Seeding"
},
{
"sbg:toolDefaultValue": "50",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--seedSearchStartLmax"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#seedSearchStartLmax",
"label": "Search start point",
"description": "Defines the search start point through the read - the read is split into pieces no longer than this value (int>0).",
"sbg:category": "Alignments and Seeding"
},
{
"sbg:toolDefaultValue": "0",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--seedSearchLmax"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#seedSearchLmax",
"label": "Max seed length",
"description": "Defines the maximum length of the seeds, if =0 max seed length is infinite (int>=0).",
"sbg:category": "Alignments and Seeding"
},
{
"sbg:toolDefaultValue": "50",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--seedPerWindowNmax"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#seedPerWindowNmax",
"label": "Max seeds per window",
"description": "Max number of seeds per window (int>=0).",
"sbg:category": "Alignments and Seeding"
},
{
"sbg:toolDefaultValue": "1000",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--seedPerReadNmax"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#seedPerReadNmax",
"label": "Max seeds per read",
"description": "Max number of seeds per read (int>=0).",
"sbg:category": "Alignments and Seeding"
},
{
"sbg:toolDefaultValue": "10",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--seedNoneLociPerWindow"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#seedNoneLociPerWindow",
"label": "Max one-seed loci per window",
"description": "Max number of one seed loci per window (int>=0).",
"sbg:category": "Alignments and Seeding"
},
{
"sbg:toolDefaultValue": "10000",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--seedMultimapNmax"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#seedMultimapNmax",
"label": "Filter pieces for stitching",
"description": "Only pieces that map fewer than this value are utilized in the stitching procedure (int>=0).",
"sbg:category": "Alignments and Seeding"
},
{
"sbg:toolDefaultValue": "1",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreStitchSJshift"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreStitchSJshift",
"label": "Max score reduction",
"description": "Maximum score reduction while searching for SJ boundaries in the stitching step.",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-2",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreInsOpen"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreInsOpen",
"label": "Insertion Open Penalty",
"description": "Insertion open penalty.",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-2",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreInsBase"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreInsBase",
"label": "Insertion extension penalty",
"description": "Insertion extension penalty per base (in addition to --scoreInsOpen).",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-0.25",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreGenomicLengthLog2scale"
},
"type": [
"null",
"float"
],
"required": false,
"id": "#scoreGenomicLengthLog2scale",
"label": "Log scaled score",
"description": "Extra score logarithmically scaled with genomic length of the alignment: <int>*log2(genomicLength).",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-8",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreGapNoncan"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreGapNoncan",
"label": "Non-canonical gap open",
"description": "Non-canonical gap open penalty (in addition to --scoreGap).",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-4",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreGapGCAG"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreGapGCAG",
"label": "GC/AG and CT/GC gap open",
"description": "GC/AG and CT/GC gap open penalty (in addition to --scoreGap).",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-8",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreGapATAC"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreGapATAC",
"label": "AT/AC and GT/AT gap open",
"description": "AT/AC and GT/AT gap open penalty (in addition to --scoreGap).",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "0",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreGap"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreGap",
"label": "Gap open penalty",
"description": "Gap open penalty.",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-2",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreDelOpen"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreDelOpen",
"label": "Deletion open penalty",
"description": "Deletion open penalty.",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "-2",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--scoreDelBase"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#scoreDelBase",
"label": "Deletion extension penalty",
"description": "Deletion extension penalty per base (in addition to --scoreDelOpen).",
"sbg:category": "Scoring"
},
{
"sbg:toolDefaultValue": "Inferred from metadata",
"type": [
"null",
"string"
],
"required": false,
"id": "#rg_seq_center",
"label": "Sequencing center",
"description": "Specify the sequencing center for RG line.",
"sbg:category": "Read group"
},
{
"sbg:toolDefaultValue": "Inferred from metadata",
"type": [
"null",
"string"
],
"required": false,
"id": "#rg_sample_id",
"label": "Sample ID",
"description": "Specify the sample ID for RG line.",
"sbg:category": "Read group"
},
{
"sbg:toolDefaultValue": "Inferred from metadata",
"type": [
"null",
"string"
],
"required": false,
"id": "#rg_platform_unit_id",
"label": "Platform unit ID",
"description": "Specify the platform unit ID for RG line.",
"sbg:category": "Read group"
},
{
"sbg:toolDefaultValue": "Inferred from metadata",
"type": [
"null",
{
"symbols": [
"LS 454",
"Helicos",
"Illumina",
"ABI SOLiD",
"Ion Torrent PGM",
"PacBio"
],
"name": "rg_platform",
"type": "enum"
}
],
"required": false,
"id": "#rg_platform",
"label": "Platform",
"description": "Specify the version of the technology that was used for sequencing or assaying.",
"sbg:category": "Read group"
},
{
"sbg:toolDefaultValue": "Inferred from metadata",
"type": [
"null",
"string"
],
"required": false,
"id": "#rg_mfl",
"label": "Median fragment length",
"description": "Specify the median fragment length for RG line.",
"sbg:category": "Read group"
},
{
"sbg:toolDefaultValue": "Inferred from metadata",
"type": [
"null",
"string"
],
"required": false,
"id": "#rg_library_id",
"label": "Library ID",
"description": "Specify the library ID for RG line.",
"sbg:category": "Read group"
},
{
"inputBinding": {
"valueFrom": {
"script": "{\n var list = [].concat($job.inputs.reads)\n var all_samples = []\n \n getUnique = function(arr){\n var u = {}, a = [];\n for(var i = 0, l = arr.length; i < l; ++i){\n if(u.hasOwnProperty(arr[i])) {\n continue;\n }\n a.push(arr[i]);\n u[arr[i]] = 1;\n }\n return a;\n }\n \n for (index = 0; index < list.length; ++index) {\n if (list[index].metadata != null){\n all_samples.push(list[index].metadata.sample_id)\n }\n }\n samples = getUnique(all_samples)\n \n var samples_given = all_samples.length == list.length\n \n for (index = 0; index < list.length; ++index) {\n if (list[index].metadata != null){\n all_samples.push(list[index].metadata.sample_id)\n }\n }\n samples = getUnique(all_samples)\n var resp = []\n \n if (list.length == 1){\n resp.push(list[0].path)\n \n }else if (list.length == 2){ \n \n left = \"\"\n right = \"\"\n \n for (index = 0; index < list.length; ++index) {\n \n if (list[index].metadata != null){\n if (list[index].metadata.paired_end == 1){\n left = list[index].path\n }else if (list[index].metadata.paired_end == 2){\n right = list[index].path\n }\n }\n }\n \n if (left != \"\" && right != \"\"){ \n resp.push(left)\n resp.push(right)\n }\n }\n else if (list.length > 2){\n left = []\n right = []\n if (samples_given){\n for (sample_ind = 0; sample_ind < samples.length; ++sample_ind){\n for (read_ind = 0; read_ind < list.length; ++read_ind){\n if (list[read_ind].metadata != null){\n if (list[read_ind].metadata.paired_end == 1 && list[read_ind].metadata.sample_id == samples[sample_ind]){\n left.push(list[read_ind].path)\n }else if (list[read_ind].metadata.paired_end == 2 && list[read_ind].metadata.sample_id == samples[sample_ind]){\n right.push(list[read_ind].path)}\n }\n }\n }\n } else {\n for (index = 0; index < list.length; ++index) {\n\n if (list[index].metadata != null){\n if (list[index].metadata.paired_end == 1){\n left.push(list[index].path)\n }else if (list[index].metadata.paired_end == 2){\n right.push(list[index].path)\n }\n }\n }\n }\n\n\n left_join = left.join()\n right_join = right.join()\n if (left != [] && right != []){ \n resp.push(left_join)\n resp.push(right_join)\n }\n }\n \n if(resp.length > 0){ \n return \"--readFilesIn \".concat(resp.join(\" \"))\n }\n}",
"class": "Expression",
"engine": "#cwl-js-engine"
},
"sbg:cmdInclude": true,
"separate": true,
"itemSeparator": " ",
"position": 10
},
"sbg:fileTypes": "FASTA, FASTQ, FA, FQ, FASTQ.GZ, FQ.GZ, FASTQ.BZ2, FQ.BZ2",
"type": [
{
"name": "reads",
"items": "File",
"type": "array"
}
],
"required": true,
"id": "#reads",
"label": "Read sequence",
"description": "Read sequence.",
"sbg:category": "Basic"
},
{
"sbg:toolDefaultValue": "NotEqual",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--readMatesLengthsIn"
},
"type": [
"null",
{
"symbols": [
"NotEqual",
"Equal"
],
"name": "readMatesLengthsIn",
"type": "enum"
}
],
"required": false,
"id": "#readMatesLengthsIn",
"label": "Reads lengths",
"description": "Equal/Not equal - lengths of names, sequences, qualities for both mates are the same/not the same. \"Not equal\" is safe in all situations.",
"sbg:category": "Read parameters"
},
{
"sbg:toolDefaultValue": "-1",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--readMapNumber"
},
"type": [
"null",
"int"
],
"required": false,
"id": "#readMapNumber",
"label": "Reads to map",
"description": "Number of reads to map from the beginning of the file.",
"sbg:category": "Read parameters"
},
{
"sbg:toolDefaultValue": "IndelSoftclipSingleend",
"inputBinding": {
"sbg:cmdInclude": true,
"separate": true,
"prefix": "--quantTranscriptomeBan"
},
"type": [
"null",
{
"symbols": [
"IndelSoftclipSingleend",
"Singleend"
],
"name": "quantTranscriptomeBan",
"type": "enum"
}
],
"required": false,
"id": "#quantTranscriptomeBan",
"label": "Prohibit alignment type",
"description": "Prohibit various alignment type. IndelSoftclipSingleend: prohibit indels, soft clipping and single-end alignments - compatible with RSEM; Singleend: prohibit single-end alignments.",
"sbg:category": "Quantification of Annotations"
},
{
"sbg:toolDefaultValue": "-",
"type": [
"null",
{
"symbols": [
"TranscriptomeSAM",
"GeneCounts",
"TranscriptomeSAM GeneCounts"
],
"name": "quantMode",
"type": "enum"
}
],
"required": false,
"id": "#quantMode",
"label": "Quantification mode",
"description": "Types of quantification requested. 'TranscriptomeSAM' option outputs SAM/BAM alignments to transcriptome into a separate file. With 'GeneCounts' option, STAR will count number of reads per gene while mapping.",
"sbg:category": "Quantification of Annotations"
},
{
"sbg:toolDefaultValue": "Unsorted",
"type": [
"null",
{