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combine multiple pytor
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parent
c183d7b397
commit
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2 changed files with 12 additions and 10 deletions
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@ -8,7 +8,7 @@ process CNVPYTOR_VIEW {
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'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(pytor)
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tuple val(meta), path(pytor_files)
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val bin_sizes
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val output_format
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@ -23,17 +23,18 @@ process CNVPYTOR_VIEW {
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script:
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def output_suffix = output_format ?: 'vcf'
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def bins = bin_sizes ?: '1000'
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def bins = bin_sizes ?: '1000'
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def input = pytor_files.join(" ")
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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python3 <<CODE
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import cnvpytor,os
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from pathlib import Path
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pytor_file = Path("$pytor")
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binsizes = "${bins}".split(" ")
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for binsize in binsizes:
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app = cnvpytor.Viewer(["$pytor"], params={} )
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outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
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file_list = "${input}".split(" ")
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app = cnvpytor.Viewer(file_list, params={} )
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outputfile = "{}_{}.{}".format("${prefix}",binsize.strip(),"${output_suffix}")
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app.print_filename = outputfile
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app.bin_size = int(binsize)
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app.print_calls_file()
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@ -47,8 +48,9 @@ process CNVPYTOR_VIEW {
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stub:
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def output_suffix = output_format ?: 'vcf'
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${pytor.baseName}.${output_suffix}
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touch ${prefix}.${output_suffix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -8,7 +8,7 @@ workflow test_cnvpytor_view {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
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[file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
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]
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bin_sizes = "10000 100000"
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@ -20,7 +20,7 @@ workflow test_cnvpytor_view_tsvout {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
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[file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
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]
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output_suffix = "tsv"
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@ -32,7 +32,7 @@ workflow test_cnvpytor_view_stub {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
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[file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
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]
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bin_sizes = []
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