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Support .bai by normalizing index name (#56)
* Support .bai by normalizing index name * Support .bai by normalizing index name * Add RNApeg+CICERO CWL workflow
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,399 @@ | ||
| { | ||
| "class": "Workflow", | ||
| "cwlVersion": "v1.1", | ||
| "label": "RNApeg + CICERO", | ||
| "inputs": [ | ||
| { | ||
| "id": "in_bam", | ||
| "sbg:fileTypes": "BAM", | ||
| "type": "File", | ||
| "label": "BAM File", | ||
| "source": "in_bam", | ||
| }, | ||
| { | ||
| "id": "in_fasta", | ||
| "sbg:fileTypes": "FA", | ||
| "type": "File", | ||
| "label": "FASTA File", | ||
| "source": "in_fasta", | ||
| }, | ||
| { | ||
| "id": "in_refflat", | ||
| "sbg:fileTypes": "TXT", | ||
| "type": "File", | ||
| "label": "RefFlaf Text File", | ||
| "source": "in_refflat", | ||
| }, | ||
| { | ||
| "id": "in_ref", | ||
| "type": "Directory", | ||
| "label": "Reference Directory", | ||
| "source": "in_refflat", | ||
| "loadListing": "deep_listing" | ||
| }, | ||
| { | ||
| "id": "in_genome", | ||
| "type": { | ||
| "type": "enum", | ||
| "symbols": [ | ||
| "GRCh37-lite", | ||
| "GRCh38_no_alt" | ||
| ], | ||
| "name": "in_genome" | ||
| }, | ||
| "label": "Genome", | ||
| "default": "GRCh38_no_alt", | ||
| }, | ||
| { | ||
| "id": "num_cores", | ||
| "type": "int?", | ||
| "label": "ncores", | ||
| "doc": "is the number of cores to be run on (with GNU parallel)", | ||
| "sbg:exposed": true | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "id": "output_file", | ||
| "outputSource": [ | ||
| "cicero/output_file" | ||
| ], | ||
| "type": "File", | ||
| } | ||
| ], | ||
| "steps": [ | ||
| { | ||
| "id": "cicero", | ||
| "in": [ | ||
| { | ||
| "id": "disable_optimize", | ||
| "default": false | ||
| }, | ||
| { | ||
| "id": "junction_file", | ||
| "source": "rnapeg/output_file" | ||
| }, | ||
| { | ||
| "id": "num_cores", | ||
| "source": "num_cores" | ||
| }, | ||
| { | ||
| "id": "bam_file", | ||
| "source": "in_bam" | ||
| }, | ||
| { | ||
| "id": "genome", | ||
| "source": "in_genome" | ||
| }, | ||
| { | ||
| "id": "refdir", | ||
| "source": "in_ref" | ||
| } | ||
| ], | ||
| "out": [ | ||
| { | ||
| "id": "output_file" | ||
| } | ||
| ], | ||
| "run": { | ||
| "class": "CommandLineTool", | ||
| "cwlVersion": "v1.1", | ||
| "id": "cicero", | ||
| "baseCommand": [ | ||
| "Cicero.sh" | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "id": "disable_optimize", | ||
| "type": "boolean?", | ||
| "inputBinding": { | ||
| "prefix": "-no-optimize", | ||
| "shellQuote": false, | ||
| "position": 100 | ||
| }, | ||
| "label": "Disable optimization", | ||
| "doc": "Disables optimizations. This can increase sensitivity, but increases the computational requirements." | ||
| }, | ||
| { | ||
| "id": "num_soft_clip", | ||
| "type": "int?", | ||
| "inputBinding": { | ||
| "prefix": "-s", | ||
| "shellQuote": false, | ||
| "position": 103 | ||
| }, | ||
| "label": "Soft Clip", | ||
| "doc": "minimum number of soft clip support required" | ||
| }, | ||
| { | ||
| "id": "threshold_soft_clip", | ||
| "type": "int?", | ||
| "inputBinding": { | ||
| "prefix": "-t", | ||
| "shellQuote": false, | ||
| "position": 102 | ||
| }, | ||
| "label": "Threshold Soft Clip", | ||
| "doc": "threshold for enabling increased soft clip cutoff" | ||
| }, | ||
| { | ||
| "id": "cluster_distance", | ||
| "type": "int?", | ||
| "inputBinding": { | ||
| "prefix": "-c", | ||
| "shellQuote": false, | ||
| "position": 104 | ||
| }, | ||
| "label": "Cluster distance", | ||
| "doc": "clustering distance for grouping similar sites" | ||
| }, | ||
| { | ||
| "id": "junction_file", | ||
| "type": "File?", | ||
| "inputBinding": { | ||
| "prefix": "-j", | ||
| "shellQuote": false, | ||
| "position": 100 | ||
| }, | ||
| "label": "Junction File", | ||
| "doc": "junctions file from RNApeg" | ||
| }, | ||
| { | ||
| "id": "num_cores", | ||
| "type": "int?", | ||
| "inputBinding": { | ||
| "prefix": "-n", | ||
| "shellQuote": false, | ||
| "position": 1 | ||
| }, | ||
| "label": "ncores", | ||
| "doc": "is the number of cores to be run on (with GNU parallel)" | ||
| }, | ||
| { | ||
| "id": "bam_file", | ||
| "type": "File", | ||
| "inputBinding": { | ||
| "prefix": "-b", | ||
| "shellQuote": false, | ||
| "position": 2 | ||
| }, | ||
| "label": "BAM File", | ||
| "doc": "input bamfile mapped to human genome builds GRCh37-lite or GRCh38_no_alt.", | ||
| "sbg:fileTypes": "BAM", | ||
| "secondaryFiles": [ | ||
| { | ||
| "pattern": ".bai?" | ||
| }, | ||
| { | ||
| "pattern": "$(self.nameroot).bai?" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "id": "genome", | ||
| "type": { | ||
| "type": "enum", | ||
| "symbols": [ | ||
| "GRCh37-lite", | ||
| "GRCh38_no_alt" | ||
| ], | ||
| "name": "genome" | ||
| }, | ||
| "inputBinding": { | ||
| "prefix": "-g", | ||
| "shellQuote": false, | ||
| "position": 3 | ||
| } | ||
| }, | ||
| { | ||
| "loadListing": "deep_listing", | ||
| "id": "refdir", | ||
| "type": "Directory", | ||
| "inputBinding": { | ||
| "prefix": "-r", | ||
| "shellQuote": false, | ||
| "position": 4 | ||
| } | ||
| }, | ||
| { | ||
| "id": "disable_excluded", | ||
| "type": "boolean?", | ||
| "inputBinding": { | ||
| "prefix": "-d", | ||
| "shellQuote": false, | ||
| "position": 104 | ||
| }, | ||
| "doc": "disable excluded regions file use" | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "id": "output_file", | ||
| "type": "File", | ||
| "outputBinding": { | ||
| "glob": "$(inputs.bam_file.nameroot)/CICERO_DATADIR/$(inputs.bam_file.nameroot)/final_fusions.txt" | ||
| } | ||
| } | ||
| ], | ||
| "label": "cicero", | ||
| "arguments": [ | ||
| { | ||
| "prefix": "-o", | ||
| "shellQuote": false, | ||
| "position": 101, | ||
| "valueFrom": "$(inputs.bam_file.nameroot)" | ||
| } | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "ShellCommandRequirement" | ||
| }, | ||
| { | ||
| "class": "LoadListingRequirement" | ||
| }, | ||
| { | ||
| "class": "ResourceRequirement", | ||
| "ramMin": 24000, | ||
| "coresMin": 2 | ||
| }, | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "hints": [ | ||
| { | ||
| "class": "DockerRequirement", | ||
| "dockerPull": "ghcr.io/stjude/cicero:latest" | ||
| } | ||
| ], | ||
| }, | ||
| "label": "cicero", | ||
| }, | ||
| { | ||
| "id": "rnapeg", | ||
| "in": [ | ||
| { | ||
| "id": "fasta", | ||
| "source": "in_fasta" | ||
| }, | ||
| { | ||
| "id": "bam_file", | ||
| "source": "in_bam" | ||
| }, | ||
| { | ||
| "id": "refFlat", | ||
| "source": "in_refflat" | ||
| } | ||
| ], | ||
| "out": [ | ||
| { | ||
| "id": "output_file" | ||
| } | ||
| ], | ||
| "run": { | ||
| "class": "CommandLineTool", | ||
| "cwlVersion": "v1.1", | ||
| "id": "rnapeg", | ||
| "baseCommand": [], | ||
| "inputs": [ | ||
| { | ||
| "id": "fasta", | ||
| "type": "File", | ||
| "inputBinding": { | ||
| "prefix": "-f", | ||
| "shellQuote": false, | ||
| "position": 32 | ||
| }, | ||
| "label": "FASTA File", | ||
| "doc": "FASTA file", | ||
| "sbg:fileTypes": "FA", | ||
| "secondaryFiles": [ | ||
| { | ||
| "pattern": ".fai" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "id": "bam_file", | ||
| "type": "File", | ||
| "inputBinding": { | ||
| "prefix": "-b", | ||
| "shellQuote": false, | ||
| "position": 2 | ||
| }, | ||
| "label": "BAM File", | ||
| "doc": "input bamfile mapped to human genome builds GRCh37-lite or GRCh38_no_alt.", | ||
| "sbg:fileTypes": "BAM", | ||
| "secondaryFiles": [ | ||
| { | ||
| "pattern": ".bai?" | ||
| }, | ||
| { | ||
| "pattern": "$(self.nameroot).bai?" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "id": "refFlat", | ||
| "type": "File", | ||
| "inputBinding": { | ||
| "prefix": "-r", | ||
| "shellQuote": false, | ||
| "position": 50 | ||
| }, | ||
| "label": "refFlat Text", | ||
| "doc": "Uncompressed refFlat.txt file from the UCSC genome annotation database", | ||
| "sbg:fileTypes": "TXT" | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "id": "output_file", | ||
| "type": "File", | ||
| "outputBinding": { | ||
| "glob": "$(inputs.bam_file.nameroot).bam.junctions.tab.shifted.tab" | ||
| } | ||
| } | ||
| ], | ||
| "label": "rnapeg", | ||
| "requirements": [ | ||
| { | ||
| "class": "ShellCommandRequirement" | ||
| }, | ||
| { | ||
| "class": "ResourceRequirement", | ||
| "ramMin": 4000, | ||
| "coresMin": 0 | ||
| }, | ||
| { | ||
| "class": "InitialWorkDirRequirement", | ||
| "listing": [ | ||
| "$(inputs.bam_file)" | ||
| ] | ||
| }, | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "hints": [ | ||
| { | ||
| "class": "DockerRequirement", | ||
| "dockerPull": "ghcr.io/stjude/rnapeg:latest" | ||
| } | ||
| ] | ||
| }, | ||
| "label": "rnapeg" | ||
| } | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "LoadListingRequirement" | ||
| }, | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| }, | ||
| { | ||
| "class": "StepInputExpressionRequirement" | ||
| } | ||
| ] | ||
| } |
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