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inutano/fastqSE2bam.packed.cwl

Created April 22, 2022 06:32
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fastqSE2bam.packed.cwl
{
"$graph": [
{
"class": "CommandLineTool",
"id": "#bwa-mem-SE.cwl",
"label": "bwa-mem-SE-0.7.12",
"hints": [
{
"class": "DockerRequirement",
"dockerPull": "biocontainers/bwa:v0.7.12_cv3"
}
],
"requirements": [
{
"class": "ShellCommandRequirement"
},
{
"class": "ResourceRequirement",
"ramMin": 6300
}
],
"baseCommand": [
"bwa",
"mem"
],
"inputs": [
{
"id": "#bwa-mem-SE.cwl/reference",
"type": "File",
"format": "http://edamontology.org/format_1929",
"inputBinding": {
"position": 4
},
"doc": "FastA file for reference genome",
"secondaryFiles": [
".amb",
".ann",
".bwt",
".pac",
".sa"
]
},
{
"id": "#bwa-mem-SE.cwl/RG_ID",
"type": "string",
"doc": "Read group identifier (ID) in RG line"
},
{
"id": "#bwa-mem-SE.cwl/RG_PL",
"type": "string",
"doc": "Platform/technology used to produce the read (PL) in RG line"
},
{
"id": "#bwa-mem-SE.cwl/RG_PU",
"type": "string",
"doc": "Platform Unit (PU) in RG line"
},
{
"id": "#bwa-mem-SE.cwl/RG_LB",
"type": "string",
"doc": "DNA preparation library identifier (LB) in RG line"
},
{
"id": "#bwa-mem-SE.cwl/RG_SM",
"type": "string",
"doc": "Sample (SM) identifier in RG line"
},
{
"id": "#bwa-mem-SE.cwl/fq",
"type": "File",
"format": "http://edamontology.org/format_1930",
"inputBinding": {
"position": 5
},
"doc": "FastQ file from next-generation sequencers"
},
{
"id": "#bwa-mem-SE.cwl/nthreads",
"type": "int",
"inputBinding": {
"prefix": "-t",
"position": 3
},
"doc": "number of cpu cores to be used"
},
{
"id": "#bwa-mem-SE.cwl/outprefix",
"type": "string"
}
],
"outputs": [
{
"id": "#bwa-mem-SE.cwl/sam",
"type": "File",
"format": "http://edamontology.org/format_2573",
"outputBinding": {
"glob": "$(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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