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combine multiple pytor

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This commit is contained in:
Ramprasad Neethiraj 2022-05-05 23:59:12 +02:00
parent c183d7b397
commit e4e4f8090c
2 changed files with 12 additions and 10 deletions
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16
modules/cnvpytor/view/main.nf
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@ -8,7 +8,7 @@ process CNVPYTOR_VIEW {
'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
input:
tuple val(meta), path(pytor)
tuple val(meta), path(pytor_files)
val bin_sizes
val output_format
@ -23,17 +23,18 @@ process CNVPYTOR_VIEW {
script:
def output_suffix = output_format ?: 'vcf'
def bins = bin_sizes ?: '1000'
def bins = bin_sizes ?: '1000'
def input = pytor_files.join(" ")
def prefix = task.ext.prefix ?: "${meta.id}"
"""
python3 <<CODE
import cnvpytor,os
from pathlib import Path
pytor_file = Path("$pytor")
binsizes = "${bins}".split(" ")
for binsize in binsizes:
app = cnvpytor.Viewer(["$pytor"], params={} )
outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
file_list = "${input}".split(" ")
app = cnvpytor.Viewer(file_list, params={} )
outputfile = "{}_{}.{}".format("${prefix}",binsize.strip(),"${output_suffix}")
app.print_filename = outputfile
app.bin_size = int(binsize)
app.print_calls_file()
@ -47,8 +48,9 @@ process CNVPYTOR_VIEW {
stub:
def output_suffix = output_format ?: 'vcf'
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${pytor.baseName}.${output_suffix}
touch ${prefix}.${output_suffix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

6
tests/modules/cnvpytor/view/main.nf
View file

@ -8,7 +8,7 @@ workflow test_cnvpytor_view {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
[file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
]
bin_sizes = "10000 100000"
@ -20,7 +20,7 @@ workflow test_cnvpytor_view_tsvout {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
[file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
]
output_suffix = "tsv"
@ -32,7 +32,7 @@ workflow test_cnvpytor_view_stub {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
[file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
]
bin_sizes = []