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April 22, 2022 06:32
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| { | |
| "$graph": [ | |
| { | |
| "class": "CommandLineTool", | |
| "id": "#bwa-mem-SE.cwl", | |
| "label": "bwa-mem-SE-0.7.12", | |
| "hints": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "biocontainers/bwa:v0.7.12_cv3" | |
| } | |
| ], | |
| "requirements": [ | |
| { | |
| "class": "ShellCommandRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "ramMin": 6300 | |
| } | |
| ], | |
| "baseCommand": [ | |
| "bwa", | |
| "mem" | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#bwa-mem-SE.cwl/reference", | |
| "type": "File", | |
| "format": "http://edamontology.org/format_1929", | |
| "inputBinding": { | |
| "position": 4 | |
| }, | |
| "doc": "FastA file for reference genome", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa" | |
| ] | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/RG_ID", | |
| "type": "string", | |
| "doc": "Read group identifier (ID) in RG line" | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/RG_PL", | |
| "type": "string", | |
| "doc": "Platform/technology used to produce the read (PL) in RG line" | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/RG_PU", | |
| "type": "string", | |
| "doc": "Platform Unit (PU) in RG line" | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/RG_LB", | |
| "type": "string", | |
| "doc": "DNA preparation library identifier (LB) in RG line" | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/RG_SM", | |
| "type": "string", | |
| "doc": "Sample (SM) identifier in RG line" | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/fq", | |
| "type": "File", | |
| "format": "http://edamontology.org/format_1930", | |
| "inputBinding": { | |
| "position": 5 | |
| }, | |
| "doc": "FastQ file from next-generation sequencers" | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/nthreads", | |
| "type": "int", | |
| "inputBinding": { | |
| "prefix": "-t", | |
| "position": 3 | |
| }, | |
| "doc": "number of cpu cores to be used" | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/outprefix", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#bwa-mem-SE.cwl/sam", | |
| "type": "File", | |
| "format": "http://edamontology.org/format_2573", | |
| "outputBinding": { | |
| "glob": "$(inputs.outprefix).sam" | |
| } | |
| }, | |
| { | |
| "id": "#bwa-mem-SE.cwl/log", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.outprefix).sam.log" | |
| } | |
| } | |
| ], | |
| "stdout": "$(inputs.outprefix).sam", | |
| "stderr": "$(inputs.outprefix).sam.log", | |
| "arguments": [ | |
| { | |
| "position": 1, | |
| "prefix": "-K", | |
| "valueFrom": "10000000" | |
| }, | |
| { | |
| "position": 2, | |
| "prefix": "-R", | |
| "valueFrom": "@RG\tID:$(inputs.RG_ID)\tPL:$(inputs.RG_PL)\tPU:$(inputs.RG_PU)\tLB:$(inputs.RG_LB)\tSM:$(inputs.RG_SM)" | |
| } | |
| ], | |
| "$namespaces": { | |
| "edam": "http://edamontology.org/" | |
| } | |
| }, | |
| { | |
| "class": "CommandLineTool", | |
| "id": "#picard-SortSam.cwl", | |
| "label": "picard-SortSam-2.10.6", | |
| "hints": [ | |
| { | |
| "class": "DockerRequirement", | |
| "dockerPull": "quay.io/biocontainers/picard:2.10.6--py27_0" | |
| } | |
| ], | |
| "requirements": [ | |
| { | |
| "class": "ShellCommandRequirement" | |
| }, | |
| { | |
| "class": "ResourceRequirement", | |
| "ramMin": 6300 | |
| } | |
| ], | |
| "baseCommand": [ | |
| "java", | |
| "-jar", | |
| "/usr/local/share/picard-2.10.6-0/picard.jar", | |
| "SortSam" | |
| ], | |
| "inputs": [ | |
| { | |
| "id": "#picard-SortSam.cwl/sam", | |
| "type": "File", | |
| "format": "http://edamontology.org/format_2573", | |
| "inputBinding": { | |
| "prefix": "INPUT=", | |
| "position": 1 | |
| }, | |
| "doc": "input SAM alignment file" | |
| }, | |
| { | |
| "id": "#picard-SortSam.cwl/outprefix", | |
| "type": "string" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#picard-SortSam.cwl/bam", | |
| "type": "File", | |
| "format": "http://edamontology.org/format_2572", | |
| "outputBinding": { | |
| "glob": "$(inputs.outprefix).bam" | |
| } | |
| }, | |
| { | |
| "id": "#picard-SortSam.cwl/log", | |
| "type": "File", | |
| "outputBinding": { | |
| "glob": "$(inputs.outprefix).bam.log" | |
| } | |
| } | |
| ], | |
| "stderr": "$(inputs.outprefix).bam.log", | |
| "arguments": [ | |
| { | |
| "position": 2, | |
| "valueFrom": "OUTPUT=$(inputs.outprefix).bam" | |
| }, | |
| { | |
| "position": 3, | |
| "valueFrom": "TMP_DIR=$(inputs.outprefix).bam.temp" | |
| }, | |
| { | |
| "position": 4, | |
| "valueFrom": "SORT_ORDER=coordinate" | |
| }, | |
| { | |
| "position": 5, | |
| "valueFrom": "COMPRESSION_LEVEL=1" | |
| }, | |
| { | |
| "position": 6, | |
| "valueFrom": "VALIDATION_STRINGENCY=LENIENT" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "Workflow", | |
| "id": "#main", | |
| "label": "fastqSE2bam", | |
| "inputs": [ | |
| { | |
| "type": "string", | |
| "doc": "Read group identifier (ID) in RG line", | |
| "id": "#RG_ID" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "DNA preparation library identifier (LB) in RG line", | |
| "id": "#RG_LB" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Platform/technology used to produce the read (PL) in RG line", | |
| "id": "#RG_PL" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Platform Unit (PU) in RG line", | |
| "id": "#RG_PU" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Sample (SM) identifier in RG line", | |
| "id": "#RG_SM" | |
| }, | |
| { | |
| "type": "File", | |
| "format": "http://edamontology.org/format_1930", | |
| "doc": "FastQ file from next-generation sequencers", | |
| "id": "#fq" | |
| }, | |
| { | |
| "type": "int", | |
| "doc": "number of cpu cores to be used", | |
| "id": "#nthreads" | |
| }, | |
| { | |
| "type": "string", | |
| "doc": "Output prefix name", | |
| "id": "#outprefix" | |
| }, | |
| { | |
| "type": "File", | |
| "format": "http://edamontology.org/format_1929", | |
| "doc": "FastA file for reference genome", | |
| "secondaryFiles": [ | |
| ".amb", | |
| ".ann", | |
| ".bwt", | |
| ".pac", | |
| ".sa" | |
| ], | |
| "id": "#reference" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "label": "bwa_mem_SE", | |
| "doc": "Mapping onto reference using BWA MEM", | |
| "run": "#bwa-mem-SE.cwl", | |
| "in": [ | |
| { | |
| "source": "#RG_ID", | |
| "id": "#bwa_mem_SE/RG_ID" | |
| }, | |
| { | |
| "source": "#RG_LB", | |
| "id": "#bwa_mem_SE/RG_LB" | |
| }, | |
| { | |
| "source": "#RG_PL", | |
| "id": "#bwa_mem_SE/RG_PL" | |
| }, | |
| { | |
| "source": "#RG_PU", | |
| "id": "#bwa_mem_SE/RG_PU" | |
| }, | |
| { | |
| "source": "#RG_SM", | |
| "id": "#bwa_mem_SE/RG_SM" | |
| }, | |
| { | |
| "source": "#fq", | |
| "id": "#bwa_mem_SE/fq" | |
| }, | |
| { | |
| "source": "#nthreads", | |
| "id": "#bwa_mem_SE/nthreads" | |
| }, | |
| { | |
| "source": "#outprefix", | |
| "id": "#bwa_mem_SE/outprefix" | |
| }, | |
| { | |
| "source": "#reference", | |
| "id": "#bwa_mem_SE/reference" | |
| } | |
| ], | |
| "out": [ | |
| "#/bwa_mem_SE/sam", | |
| "#/bwa_mem_SE/log" | |
| ], | |
| "id": "#bwa_mem_SE" | |
| }, | |
| { | |
| "label": "picard_SortSam", | |
| "doc": "Sort sam file and save as bam file", | |
| "run": "#picard-SortSam.cwl", | |
| "in": [ | |
| { | |
| "source": "#outprefix", | |
| "id": "#picard_SortSam/outprefix" | |
| }, | |
| { | |
| "source": "#/bwa_mem_SE/sam", | |
| "id": "#picard_SortSam/sam" | |
| } | |
| ], | |
| "out": [ | |
| "#/picard_SortSam/bam", | |
| "#/picard_SortSam/log" | |
| ], | |
| "id": "#picard_SortSam" | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "type": "File", | |
| "format": "http://edamontology.org/format_2572", | |
| "outputSource": "#/picard_SortSam/bam", | |
| "id": "#bam" | |
| }, | |
| { | |
| "type": "File", | |
| "outputSource": "#/picard_SortSam/log", | |
| "id": "#bam_log" | |
| }, | |
| { | |
| "type": "File", | |
| "format": "http://edamontology.org/format_2573", | |
| "outputSource": "#/bwa_mem_SE/sam", | |
| "id": "#sam" | |
| }, | |
| { | |
| "type": "File", | |
| "outputSource": "#/bwa_mem_SE/log", | |
| "id": "#sam_log" | |
| } | |
| ] | |
| } | |
| ], | |
| "cwlVersion": "v1.0" | |
| } |
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