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Merge branch 'master' into modules/md5sum

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Jose Espinosa-Carrasco 2022-05-06 12:34:14 +02:00 committed by GitHub
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6 changed files with 20 additions and 19 deletions
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1
modules/cnvpytor/callcnvs/main.nf
View file

@ -20,7 +20,6 @@ process CNVPYTOR_CALLCNVS {
script: script:
def bins = bin_sizes ?: '1000' def bins = bin_sizes ?: '1000'
def prefix = task.ext.prefix ?: "${meta.id}"
""" """
cnvpytor \\ cnvpytor \\
-root $pytor \\ -root $pytor \\

16
modules/cnvpytor/view/main.nf
View file

@ -8,7 +8,7 @@ process CNVPYTOR_VIEW {
'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }" 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(pytor) tuple val(meta), path(pytor_files)
val bin_sizes val bin_sizes
val output_format val output_format
@ -23,17 +23,18 @@ process CNVPYTOR_VIEW {
script: script:
def output_suffix = output_format ?: 'vcf' 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 ?: "${meta.id}"
""" """
python3 <<CODE python3 <<CODE
import cnvpytor,os import cnvpytor,os
from pathlib import Path
pytor_file = Path("$pytor")
binsizes = "${bins}".split(" ") binsizes = "${bins}".split(" ")
for binsize in binsizes: for binsize in binsizes:
app = cnvpytor.Viewer(["$pytor"], params={} ) file_list = "${input}".split(" ")
outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}") app = cnvpytor.Viewer(file_list, params={} )
outputfile = "{}_{}.{}".format("${prefix}",binsize.strip(),"${output_suffix}")
app.print_filename = outputfile app.print_filename = outputfile
app.bin_size = int(binsize) app.bin_size = int(binsize)
app.print_calls_file() app.print_calls_file()
@ -47,8 +48,9 @@ process CNVPYTOR_VIEW {
stub: stub:
def output_suffix = output_format ?: 'vcf' def output_suffix = output_format ?: 'vcf'
def prefix = task.ext.prefix ?: "${meta.id}"
""" """
touch ${pytor.baseName}.${output_suffix} touch ${prefix}.${output_suffix}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

4
modules/cnvpytor/view/meta.yml
View file

@ -17,9 +17,9 @@ input:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test' ] e.g. [ id:'test' ]
- pytor: - pytor_files:
type: file type: file
description: pytor file containing read depth data description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files.
pattern: "*.{pytor}" pattern: "*.{pytor}"
- bin_sizes: - bin_sizes:
type: string type: string

6
modules/svdb/merge/main.nf
View file

@ -2,10 +2,10 @@ process SVDB_MERGE {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null) conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0': 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0':
'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }" 'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }"
input: input:
tuple val(meta), path(vcfs) tuple val(meta), path(vcfs)

6
modules/svdb/query/main.nf
View file

@ -2,10 +2,10 @@ process SVDB_QUERY {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null) conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0': 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0':
'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }" 'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

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

@ -8,7 +8,7 @@ workflow test_cnvpytor_view {
input = [ input = [
[ id:'test'], // meta map [ 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" bin_sizes = "10000 100000"
@ -20,7 +20,7 @@ workflow test_cnvpytor_view_tsvout {
input = [ input = [
[ id:'test'], // meta map [ 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" output_suffix = "tsv"
@ -32,7 +32,7 @@ workflow test_cnvpytor_view_stub {
input = [ input = [
[ id:'test'], // meta map [ 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 = [] bin_sizes = []