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workflow1_11.cwl
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workflow1_11.cwl
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#!/usr/bin/env cwl-runner
{
"cwlVersion": "v1.0",
"$graph": [
{
"inputs": [
{
"inputBinding": {
"prefix": "--annot-r1",
"itemSeparator": ","
},
"type": {
"items": "File",
"type": "array"
},
"id": "#AddtoBam.cwl/Annotation_R1"
},
{
"inputBinding": {
"prefix": "--cell-order"
},
"type": "File",
"id": "#AddtoBam.cwl/Cell_Order"
},
{
"inputBinding": {
"prefix": "--annot-mol-file"
},
"type": "File",
"id": "#AddtoBam.cwl/Molecular_Annotation"
},
{
"inputBinding": {
"prefix": "--r2-bam"
},
"type": "File",
"id": "#AddtoBam.cwl/R2_Bam"
},
{
"inputBinding": {
"prefix": "--run-metadata"
},
"type": "File",
"id": "#AddtoBam.cwl/Run_Metadata"
},
{
"inputBinding": {
"prefix": "--tag-calls"
},
"type": [
"null",
"File"
],
"id": "#AddtoBam.cwl/Tag_Calls"
},
{
"inputBinding": {
"prefix": "--target-gene-mapping"
},
"type": [
"null",
"File"
],
"id": "#AddtoBam.cwl/Target_Gene_Mapping"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
}
],
"outputs": [
{
"outputBinding": {
"glob": "Annotated_mapping_R2.BAM"
},
"type": "File",
"id": "#AddtoBam.cwl/Annotated_Bam"
},
{
"outputBinding": {
"glob": "*.log"
},
"type": "File",
"id": "#AddtoBam.cwl/output"
}
],
"baseCommand": [
"mist_add_to_bam.py"
],
"class": "CommandLineTool",
"id": "#AddtoBam.cwl"
},
{
"inputs": [
{
"inputBinding": {
"prefix": "--extra-seqs"
},
"type": [
"null",
"File"
],
"id": "#AlignR2.cwl/Extra_Seqs"
},
{
"inputBinding": {
"prefix": "--index"
},
"type": "File",
"id": "#AlignR2.cwl/Index"
},
{
"inputBinding": {
"prefix": "--r2-fastqs",
"itemSeparator": ","
},
"type": {
"items": "File",
"type": "array"
},
"id": "#AlignR2.cwl/R2"
},
{
"inputBinding": {
"prefix": "--run-metadata"
},
"type": "File",
"id": "#AlignR2.cwl/Run_Metadata"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
},
{
"class": "InlineJavascriptRequirement"
},
{
"envDef": [
{
"envName": "CORES_ALLOCATED_PER_CWL_PROCESS",
"envValue": "$(String(runtime.cores))"
}
],
"class": "EnvVarRequirement"
}
],
"outputs": [
{
"outputBinding": {
"glob": "*zip"
},
"type": {
"items": "File",
"type": "array"
},
"id": "#AlignR2.cwl/Alignments"
},
{
"outputBinding": {
"glob": "*.log"
},
"type": "File",
"id": "#AlignR2.cwl/output"
}
],
"baseCommand": [
"mist_align_R2.py"
],
"class": "CommandLineTool",
"id": "#AlignR2.cwl"
},
{
"inputs": [
{
"inputBinding": {
"prefix": "--umi-option"
},
"type": [
"null",
"int"
],
"id": "#AnnotateMolecules.cwl/AbSeq_UMI"
},
{
"inputBinding": {
"prefix": "--run-metadata"
},
"type": "File",
"id": "#AnnotateMolecules.cwl/Run_Metadata"
},
{
"inputBinding": {
"prefix": "--use-dbec"
},
"type": [
"null",
"boolean"
],
"id": "#AnnotateMolecules.cwl/Use_DBEC"
},
{
"inputBinding": {
"prefix": "--valid-annot"
},
"type": "File",
"id": "#AnnotateMolecules.cwl/Valids"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
}
],
"outputs": [
{
"outputBinding": {
"glob": "*_GeneStatus.csv.*"
},
"type": "File",
"id": "#AnnotateMolecules.cwl/Gene_Status_List"
},
{
"outputBinding": {
"glob": "stats.json",
"loadContents": true,
"outputEval": "$(JSON.parse(self[0].contents).max_count)\n"
},
"type": "int",
"id": "#AnnotateMolecules.cwl/Max_Count"
},
{
"outputBinding": {
"glob": "*_Annotation_Molecule.csv.*"
},
"type": "File",
"id": "#AnnotateMolecules.cwl/Mol_Annot_List"
},
{
"outputBinding": {
"glob": "stats.json",
"loadContents": true,
"outputEval": "$(JSON.parse(self[0].contents).total_molecules)\n"
},
"type": "int",
"id": "#AnnotateMolecules.cwl/Total_Molecules"
},
{
"outputBinding": {
"glob": "*.log"
},
"type": "File",
"id": "#AnnotateMolecules.cwl/output"
}
],
"baseCommand": [
"mist_annotate_molecules.py"
],
"class": "CommandLineTool",
"id": "#AnnotateMolecules.cwl"
},
{
"inputs": [
{
"inputBinding": {
"prefix": "--filter-metrics",
"itemSeparator": ","
},
"type": [
{
"items": [
"null",
"File"
],
"type": "array"
}
],
"id": "#AnnotateR1.cwl/Filter_Metrics"
},
{
"inputBinding": {
"prefix": "--R1"
},
"type": "File",
"id": "#AnnotateR1.cwl/R1"
},
{
"inputBinding": {
"prefix": "--run-metadata"
},
"type": "File",
"id": "#AnnotateR1.cwl/Run_Metadata"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
},
{
"ramMin": 2000,
"class": "ResourceRequirement"
}
],
"outputs": [
{
"outputBinding": {
"glob": "*_Annotation_R1.csv.gz"
},
"type": "File",
"id": "#AnnotateR1.cwl/Annotation_R1"
},
{
"outputBinding": {
"glob": "*_R1_error_count_table.npy"
},
"type": "File",
"id": "#AnnotateR1.cwl/R1_error_count_table"
},
{
"outputBinding": {
"glob": "*_R1_read_count_breakdown.json"
},
"type": "File",
"id": "#AnnotateR1.cwl/R1_read_count_breakdown"
},
{
"outputBinding": {
"glob": "*.log"
},
"type": "File",
"id": "#AnnotateR1.cwl/output"
}
],
"baseCommand": [
"mist_annotate_R1.py"
],
"class": "CommandLineTool",
"id": "#AnnotateR1.cwl"
},
{
"inputs": [
{
"inputBinding": {
"prefix": "--extra-seqs"
},
"type": [
"null",
"File"
],
"id": "#AnnotateR2.cwl/Extra_Seqs"
},
{
"inputBinding": {
"prefix": "--gtf"
},
"type": [
"null",
"File"
],
"id": "#AnnotateR2.cwl/GTF_Annotation"
},
{
"inputBinding": {
"prefix": "--R2-zip"
},
"type": "File",
"id": "#AnnotateR2.cwl/R2_zip"
},
{
"inputBinding": {
"prefix": "--run-metadata"
},
"type": "File",
"id": "#AnnotateR2.cwl/Run_Metadata"
},
{
"inputBinding": {
"prefix": "--transcript-length"
},
"type": [
"null",
"File"
],
"id": "#AnnotateR2.cwl/Transcript_Length"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
},
{
"class": "InlineJavascriptRequirement"
}
],
"outputs": [
{
"outputBinding": {
"glob": "*Annotation_R2.csv.gz"
},
"type": "File",
"id": "#AnnotateR2.cwl/Annot_R2"
},
{
"outputBinding": {
"glob": "*-annot.gtf"
},
"type": [
"null",
"File"
],
"id": "#AnnotateR2.cwl/GTF"
},
{
"outputBinding": {
"glob": "*mapping_R2.BAM"
},
"type": "File",
"id": "#AnnotateR2.cwl/R2_Bam"
},
{
"outputBinding": {
"glob": "*_picard_quality_metrics.csv.gz"
},
"type": "File",
"id": "#AnnotateR2.cwl/R2_Quality_Metrics"
},
{
"outputBinding": {
"glob": "*.log"
},
"type": "File",
"id": "#AnnotateR2.cwl/output"
}
],
"baseCommand": [
"mist_annotate_R2.py"
],
"class": "CommandLineTool",
"id": "#AnnotateR2.cwl"
},
{
"inputs": [
{
"inputBinding": {
"prefix": "--umi-option"
},
"type": [
"null",
"int"
],
"id": "#AnnotateReads.cwl/AbSeq_UMI"
},
{
"inputBinding": {
"prefix": "--extra-seqs",
"itemSeparator": ","
},
"type": [
"null",
"File"
],
"id": "#AnnotateReads.cwl/Extra_Seqs"
},
{
"type": {
"items": [
"null",
"File"
],
"type": "array"
},
"id": "#AnnotateReads.cwl/Filter_Metrics"
},
{
"inputBinding": {
"prefix": "--putative-cell-call"
},
"type": [
"null",
"int"
],
"id": "#AnnotateReads.cwl/Putative_Cell_Call"
},
{
"type": {
"items": "File",
"type": "array"
},
"id": "#AnnotateReads.cwl/R1_Annotation"
},
{
"type": {
"items": "File",
"type": "array"
},
"id": "#AnnotateReads.cwl/R1_error_count_table"
},
{
"type": {
"items": "File",
"type": "array"
},
"id": "#AnnotateReads.cwl/R1_read_count_breakdown"
},
{
"type": {
"items": "File",
"type": "array"
},
"id": "#AnnotateReads.cwl/R2_Annotation"
},
{
"type": {
"items": "File",
"type": "array"
},
"id": "#AnnotateReads.cwl/R2_Quality_Metrics"
},
{
"inputBinding": {
"prefix": "--run-metadata"
},
"type": "File",
"id": "#AnnotateReads.cwl/Run_Metadata"
},
{
"inputBinding": {
"prefix": "--target-gene-mapping"
},
"type": [
"null",
"File"
],
"id": "#AnnotateReads.cwl/Target_Gene_Mapping"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
},
{
"class": "InitialWorkDirRequirement",
"listing": [
{
"writable": false,
"entry": "${\n function getPaths(inputs, attribute) {\n var fp_arr = []\n for (var i = 0; i < inputs[attribute].length; i++)\n {\n fp_arr.push(inputs[attribute][i].path);\n }\n return fp_arr;\n }\n var paths = {}\n paths['annotR1'] = getPaths(inputs, 'R1_Annotation')\n paths['R1_error_count_table'] = getPaths(inputs, 'R1_error_count_table')\n paths['R1_read_count_breakdown'] = getPaths(inputs, 'R1_read_count_breakdown')\n paths['annotR2'] = getPaths(inputs, 'R2_Annotation')\n paths['r2_quality_metrics_fps'] = getPaths(inputs, 'R2_Quality_Metrics')\n if(inputs.Filter_Metrics[0] != null){\n paths['filtering_stat_files'] = getPaths(inputs, 'Filter_Metrics')\n }\n var paths_json = JSON.stringify(paths);\n return paths_json;\n}",
"entryname": "manifest.json"
}
]
},
{
"class": "InlineJavascriptRequirement"
},
{
"envDef": [
{
"envName": "CORES_ALLOCATED_PER_CWL_PROCESS",
"envValue": "4"
}
],
"class": "EnvVarRequirement"
}
],
"outputs": [
{
"outputBinding": {
"glob": "*_Annotation_Read.csv.gz"
},
"type": [
"null",
"File"
],
"id": "#AnnotateReads.cwl/Annotation_Read"
},
{
"outputBinding": {
"glob": "*read1_error_rate_archive*"
},
"type": "File",
"id": "#AnnotateReads.cwl/Read1_error_rate"
},
{
"outputBinding": {
"glob": "*_SeqMetrics.csv.gz"
},
"type": "File",
"id": "#AnnotateReads.cwl/Seq_Metrics"
},
{
"outputBinding": {
"glob": "*Sorted_Valid_Reads.csv.*"
},
"type": {
"items": "File",
"type": "array"
},
"id": "#AnnotateReads.cwl/Valid_Reads"
},
{
"outputBinding": {
"glob": "num_vdj_reads.json",
"loadContents": true,
"outputEval": "${ if (!self[0]) { return 0; } return parseInt(JSON.parse(self[0].contents).BCR); }"
},
"type": "int",
"id": "#AnnotateReads.cwl/num_valid_ig_reads"
},
{
"outputBinding": {
"glob": "num_vdj_reads.json",
"loadContents": true,
"outputEval": "${ if (!self[0]) { return 0; } return parseInt(JSON.parse(self[0].contents).TCR); }"
},
"type": "int",
"id": "#AnnotateReads.cwl/num_valid_tcr_reads"
},
{
"outputBinding": {
"glob": "*.log"
},
"type": "File",
"id": "#AnnotateReads.cwl/output"
},
{
"outputBinding": {
"glob": "*_VDJ_IG_Valid_Reads.fastq.gz"
},
"type": [
"null",
"File"
],
"id": "#AnnotateReads.cwl/validIgReads"
},
{
"outputBinding": {
"glob": "*_VDJ_TCR_Valid_Reads.fastq.gz"
},
"type": [
"null",
"File"
],
"id": "#AnnotateReads.cwl/validTcrReads"
}
],
"baseCommand": [
"mist_annotate_reads.py"
],
"class": "CommandLineTool",
"id": "#AnnotateReads.cwl"
},
{
"inputs": [
{
"type": {
"items": "File",
"type": "array"
},
"id": "#BundleLogs.cwl/log_files"
}
],
"requirements": [
{
"class": "InlineJavascriptRequirement"
},
{
"class": "MultipleInputFeatureRequirement"
}
],
"outputs": [
{
"type": "Directory",
"id": "#BundleLogs.cwl/logs_dir"
}
],
"class": "ExpressionTool",
"expression": "${\n /* shamelly cribbed from https://gist.github.com/jcxplorer/823878 */\n function uuid() {\n var uuid = \"\", i, random;\n for (i = 0; i < 32; i++) {\n random = Math.random() * 16 | 0;\n if (i == 8 || i == 12 || i == 16 || i == 20) {\n uuid += \"-\";\n }\n uuid += (i == 12 ? 4 : (i == 16 ? (random & 3 | 8) : random)).toString(16);\n }\n return uuid;\n }\n var listing = [];\n for (var i = 0; i < inputs.log_files.length; i++) {\n var log_file = inputs.log_files[i];\n log_file.basename = uuid() + \"-\" + log_file.basename;\n listing.push(log_file);\n }\n return ({\n logs_dir: {\n class: \"Directory\",\n basename: \"Logs\",\n listing: listing\n }\n });\n}",
"id": "#BundleLogs.cwl"
},
{
"inputs": [
{
"doc": "The minimum size (megabytes) of a file that should get split into chunks of a size designated in NumRecordsPerSplit\n",
"inputBinding": {
"prefix": "--min-split-size"
},
"type": [
"null",
"int"
],
"id": "#CheckFastqs.cwl/MinChunkSize"
},
{
"inputBinding": {
"prefix": "--reads",
"itemSeparator": ","
},
"type": {
"items": "File",
"type": "array"
},
"id": "#CheckFastqs.cwl/Reads"
},
{
"inputBinding": {
"prefix": "--subsample-reads"
},
"type": [
"null",
"float"
],
"id": "#CheckFastqs.cwl/Subsample_Reads"
},
{
"inputBinding": {
"prefix": "--subsample-seed"
},
"type": [
"null",
"int"
],
"id": "#CheckFastqs.cwl/Subsample_Seed"
},
{
"inputBinding": {
"prefix": "--subsample-seed"
},
"type": [
"null",
"int"
],
"id": "#CheckFastqs.cwl/UserInputSubsampleSeed"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
},
{
"class": "InlineJavascriptRequirement"
}
],
"doc": "CheckFastqs does several quality control routines including: (1) ensuring that read pair file names are formatted correctly and contain a read pair mate; (2) disambiguating the \"Subsample Reads\" input and; (3) if not provided, generating a subsampling seed that the downstream instances can use.\n",
"baseCommand": [
"mist_check_fastqs.py"
],
"id": "#CheckFastqs.cwl",
"outputs": [
{
"outputBinding": {
"glob": "bead_version.json",
"loadContents": true,
"outputEval": "$(JSON.parse(self[0].contents).BeadVersion)\n"
},
"type": {
"items": {
"fields": [
{
"type": "string",
"name": "#CheckFastqs.cwl/Bead_Version/Library"
},
{
"type": "string",
"name": "#CheckFastqs.cwl/Bead_Version/bead_version"
}
],
"type": "record"
},
"type": "array"
},
"id": "#CheckFastqs.cwl/Bead_Version"
},
{
"outputBinding": {
"glob": "fastq_read_pairs.json",
"loadContents": true,
"outputEval": "$(JSON.parse(self[0].contents).fastq_read_pairs)\n"
},
"type": {
"items": {
"fields": [
{
"type": "string",
"name": "#CheckFastqs.cwl/FastqReadPairs/filename"
},
{
"type": "string",
"name": "#CheckFastqs.cwl/FastqReadPairs/readFlag"
},
{
"type": "string",
"name": "#CheckFastqs.cwl/FastqReadPairs/readPairId"
},
{
"type": "string",
"name": "#CheckFastqs.cwl/FastqReadPairs/library"
},
{
"type": "string",
"name": "#CheckFastqs.cwl/FastqReadPairs/beadVersion"
}
],
"type": "record"
},
"type": "array"
},
"id": "#CheckFastqs.cwl/FastqReadPairs"
},
{
"outputBinding": {
"glob": "files_to_skip_split_and_subsample.json",
"loadContents": true,
"outputEval": "$(JSON.parse(self[0].contents).files_to_skip_split_and_subsample)\n"
},
"type": {
"items": "string",
"type": "array"
},
"id": "#CheckFastqs.cwl/FilesToSkipSplitAndSubsample"
},
{
"outputBinding": {
"glob": "fastq_read_pairs.json",
"loadContents": true,
"outputEval": "${\n var obj = JSON.parse(self[0].contents);\n var libraries = [];\n var pairs = obj.fastq_read_pairs\n for (var i in pairs){\n if (pairs[i][\"readFlag\"] == \"R1\"){\n if (libraries.indexOf(pairs[i][\"library\"]) == -1){ \n libraries.push(pairs[i][\"library\"]);\n }\n }\n }\n libraries.sort();\n return(libraries.toString())\n}\n"
},
"type": [
"null",
"string"
],
"id": "#CheckFastqs.cwl/Libraries"
},
{
"outputBinding": {
"outputEval": "${ \n var reads = []; \n var files = inputs.Reads\n for (var i in files){\n reads.push(files[i][\"basename\"]);\n }\n reads.sort();\n return(reads)\n}\n"
},
"type": [
"null",
{
"items": "string",
"type": "array"
}
],
"id": "#CheckFastqs.cwl/ReadsList"
},
{
"outputBinding": {
"glob": "subsampling_info.json",
"loadContents": true,
"outputEval": "$(JSON.parse(self[0].contents).subsampling_seed)\n"
},
"type": "int",
"id": "#CheckFastqs.cwl/SubsampleSeed"
},
{
"outputBinding": {
"glob": "subsampling_info.json",
"loadContents": true,
"outputEval": "$(JSON.parse(self[0].contents).subsampling_ratio)\n"
},
"type": "float",
"id": "#CheckFastqs.cwl/SubsamplingRatio"
},
{
"outputBinding": {
"glob": "*.log"
},
"type": "File",
"id": "#CheckFastqs.cwl/log"
}
],
"class": "CommandLineTool"
},
{
"inputs": [
{
"inputBinding": {
"prefix": "--abseq-reference",
"itemSeparator": ","
},
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"id": "#CheckReference.cwl/AbSeq_Reference"
},
{
"inputBinding": {
"prefix": "--putative-cell-call"
},
"type": [
"null",
"int"
],
"id": "#CheckReference.cwl/Putative_Cell_Call"
},
{
"inputBinding": {
"prefix": "--reference",
"itemSeparator": ","
},
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"id": "#CheckReference.cwl/Reference"
},
{
"inputBinding": {
"prefix": "--run-metadata"
},
"type": "File",
"id": "#CheckReference.cwl/Run_Metadata"
},
{
"inputBinding": {
"prefix": "--supplemental-reference",
"itemSeparator": ","
},
"type": [
"null",
{
"items": "File",
"type": "array"
}
],
"id": "#CheckReference.cwl/Supplemental_Reference"
}
],
"requirements": [
{
"dockerPull": "docker.io/bdgenomics/rhapsody:1.11",
"class": "DockerRequirement"
},
{
"class": "InlineJavascriptRequirement"
}
],
"outputs": [
{
"outputBinding": {
"glob": "combined_extra_seq.fasta"
},
"type": [
"null",
"File"
],
"id": "#CheckReference.cwl/Extra_Seqs"
},
{
"outputBinding": {
"glob": "full-gene-list.json"
},
"type": [
"null",
"File"
],
"id": "#CheckReference.cwl/Full_Genes"
},
{
"outputBinding": {
"glob": "*gtf",
"outputEval": "${\n // get the WTA modified GTF with extra seqs\n if (self.length == 1) {\n return self;\n // there is no modified GTF\n } else if (self.length == 0) {\n // if Reference is null (i.e. AbSeq_Reference only), return no GTF\n if (inputs.Reference === null) {\n return null;\n } else {\n // get the original WTA GTF without extra seqs\n for (var i = 0; i < inputs.Reference.length; i++) {\n if (inputs.Reference[i].basename.toLowerCase().indexOf('gtf') !== -1) {\n return inputs.Reference[i];\n }\n }\n // return no GTF for Targeted\n return null\n }\n }\n}\n"
},
"type": [
"null",
"File"
],
"id": "#CheckReference.cwl/GTF"
},
{
"outputBinding": {
"glob": "*-annot.*",
"outputEval": "${\n if (self.length == 1) { // Targeted\n return self;\n } else if (self.length == 0){ // WTA without extra seqs or targets\n for (var i = 0; i < inputs.Reference.length; i++) {\n if (inputs.Reference[i].basename.toLowerCase().indexOf('tar.gz') !== -1) {\n return inputs.Reference[i];\n }\n }\n return null\n }\n}\n"
},
"type": "File",
"id": "#CheckReference.cwl/Index"
},
{
"outputBinding": {
"glob": "target-gene.json"
},
"type": [
"null",
"File"
],
"id": "#CheckReference.cwl/Target_Gene_Mapping"