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05-viGEN.json
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{
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"label": "Report all alignments",
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{
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"label": "Alignment metrics",
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"id": "#metrics",
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},
{
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"label": "Ignore qualities",
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"sbg:category": "Alignment",
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{
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}
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"outputs": [
{
"label": "idxstats_metrics",
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"sbg:includeInPorts": true,
"id": "#output_indexed_file",
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"sbg:canvas_zoom": 0.7999999999999998,
"description": "For comparison with Centrifuge and Kraken",
"sbg:projectName": "Viral_cervival_Cancer",
"label": "Viral alignment-FINAL-with-decompressor-FOR-COMPARISON",
"class": "Workflow",
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"steps": [
{
"inputs": [
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{
"id": "#SAMtools_Index_BAM_CRAM.input_index_file"
},
{
"source": [
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],
"id": "#SAMtools_Index_BAM_CRAM.input_bam_or_cram_file"
},
{
"id": "#SAMtools_Index_BAM_CRAM.bai_index",
"default": true
}
],
"outputs": [
{
"id": "#SAMtools_Index_BAM_CRAM.output_indexed_file"
},
{
"id": "#SAMtools_Index_BAM_CRAM.generated_index"
}
],
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"run": {
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"inputs": [
{
"label": "output indexed data file",
"description": "Don't output indexed data file. The default value is [FALSE].",
"sbg:category": "Input & Output",
"id": "#output_indexed_data",
"required": false,
"type": [
"null",
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]
},
{
"label": "Input index file",
"description": "Input index file (CSI, CRI, or BAI).",
"sbg:category": "File input",
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"sbg:stageInput": "link",
"id": "#input_index_file",
"required": false,
"type": [
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},
{
"label": "BAM/ Cram input file",
"description": "BAM/ Cram input file.",
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"sbg:stageInput": "copy",
"id": "#input_bam_or_cram_file",
"required": true,
"type": [
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]
},
{
"label": "Create a BAI index",
"description": "Create a BAI index. This is currently the default when no format options are used.",
"sbg:category": "configuration",
"inputBinding": {
"separate": true,
"sbg:cmdInclude": true,
"valueFrom": {
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "{\n if ($job.inputs.bai_index)\n {\n if ($job.inputs.input_index_file)\n {\n index_exe = $job.inputs.input_index_file.path.substr($job.inputs.input_index_file.path.lastIndexOf('.')+1)\n\n inp_exe = $job.inputs.input_bam_or_cram_file.path.substr($job.inputs.input_bam_or_cram_file.path.lastIndexOf('.')+1)\n\n if (!((index_exe.toUpperCase() === 'CRAI' && inp_exe.toUpperCase() === 'CRAM') ||\n (index_exe.toUpperCase() === 'BAI' && inp_exe.toUpperCase() === 'BAM' ) ))\n {\n return \"-b\"\n }\n }\n else\n {\n return \"-b\"\n }\n\n }\n}"
}
},
"id": "#bai_index",
"required": false,
"type": [
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"sbg:modifiedOn": 1476440186,
"stdout": "",
"requirements": [
{
"class": "ExpressionEngineRequirement",
"id": "#cwl-js-engine",
"requirements": [
{
"class": "DockerRequirement",
"dockerPull": "rabix/js-engine"
}
]
}
],
"x": 1041.2498372395808,
"sbg:revisionNotes": "Add common issue.",
"arguments": [],
"sbg:toolkitVersion": "v1.3",
"sbg:validationErrors": [],
"cwlVersion": "sbg:draft-2",
"sbg:createdBy": "djordje_klisic",
"label": "SAMtools Index BAM/CRAM",
"sbg:revision": 17,
"temporaryFailCodes": [],
"sbg:id": "admin/sbg-public-data/samtools-index-bam-1-3/17",
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"id": "admin/sbg-public-data/samtools-index-bam-1-3/17",
"sbg:job": {
"inputs": {
"bai_index": false,
"output_indexed_data": true,
"input_bam_or_cram_file": {
"class": "File",
"secondaryFiles": [],
"size": 0,
"path": "input2.cram"
}
},
"allocatedResources": {
"cpu": 1,
"mem": 1000
}
},
"sbg:sbgMaintained": false,
"outputs": [
{
"label": "Output indexed File",
"description": "Output BAM, CRAM, along with index as secondary file.",
"outputBinding": {
"glob": {
"class": "Expression",
"engine": "#cwl-js-engine",
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},
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},
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"id": "#output_indexed_file",
"sbg:fileTypes": "BAM"
},
{
"label": "Generated index",
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},
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],
"id": "#generated_index",
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}
],
"sbg:links": [
{
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"id": "http://samtools.sourceforge.net/"
},
{
"label": "Source code",
"id": "https://github.com/samtools/samtools"
},
{
"label": "Wiki",
"id": "http://sourceforge.net/p/samtools/wiki/Home/"
},
{
"label": "Download",
"id": "http://sourceforge.net/projects/samtools/files/"
},
{
"label": "Publication",
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{
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}
],
"baseCommand": [
{
"class": "Expression",
"engine": "#cwl-js-engine",
"script": "{\n \n if ($job.inputs.input_index_file)\n {\n index_exe = $job.inputs.input_index_file.path.substr($job.inputs.input_index_file.path.lastIndexOf('.')+1)\n \n inp_exe = $job.inputs.input_bam_or_cram_file.path.substr($job.inputs.input_bam_or_cram_file.path.lastIndexOf('.')+1)\n \n if(index_exe.toUpperCase() === 'CRAI' && inp_exe.toUpperCase() === 'CRAM')\n {\n return\"echo Skipping index step because BAI file is provided on the input.\"\n } \n else if(index_exe.toUpperCase() === 'BAI' && inp_exe.toUpperCase() === 'BAM' ) \n {\n return\"echo Skipping index step because BAI file is provided on the input.\" \n }\n \telse\n {\n return \"/opt/samtools-1.3/samtools index\" +\" \" + $job.inputs.input_bam_or_cram_file.path\n }\n }\n else\n {\n return \"/opt/samtools-1.3/samtools index\" +\" \" + $job.inputs.input_bam_or_cram_file.path\n } \n}"
}
],
"sbg:cmdPreview": "/opt/samtools-1.3/samtools index input2.cram",
"description": "SAMtools Index BAM indexes sorted alignments for fast random access. Index file <aln.bam>.bai is created.\n\n###Common issue:\nFiles should be sorted by coordinates not by name, otherwise the tool output will be empty since SAMtools exits without returning error code.",
"sbg:projectName": "SBG Public data",
"class": "CommandLineTool",
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"successCodes": [],
"sbg:contributors": [
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],
"sbg:categories": [
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"Indexing"
],
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"prefix": "--skip"
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{
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"description": "Set the seed for pseudo-random number generator.",
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"prefix": "--seed"
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"sbg:toolDefaultValue": "0 for \"End-to-end\" mode, 2 for \"Local\" mode",
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},
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