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bwa-mem.cwl
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bwa-mem.cwl
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{
"hints": [
{
"dockerPull": "duplexa/4dn-hic:v42.1",
"class": "DockerRequirement"
}
],
"arguments": [],
"class": "CommandLineTool",
"inputs": [
{
"type": [
"File"
],
"id": "#fastq1",
"inputBinding": {
"position": 1,
"separate": true
}
},
{
"type": [
"File"
],
"id": "#fastq2",
"inputBinding": {
"position": 2,
"separate": true
}
},
{
"type": [
"File"
],
"id": "#bwa_index",
"inputBinding": {
"position": 3,
"separate": true
}
},
{
"type": [
"int"
],
"id": "#nThreads",
"inputBinding": {
"position": 6,
"separate": true
},
"default": 4
},
{
"type": [
"null",
"string"
],
"id": "#prefix",
"inputBinding": {
"position": 5,
"separate": true
},
"default": "out"
},
{
"type": [
"null",
"string"
],
"id": "#outdir",
"inputBinding": {
"position": 4,
"separate": true
},
"default": "."
}
],
"outputs": [
{
"type": [
"null",
"File"
],
"id": "#out_bam",
"outputBinding": {
"glob": "*.bam"
}
}
],
"baseCommand": [
"run-bwa-mem.sh"
],
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"cwlVersion": "v1.0"
}