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fix untar output dir

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This commit is contained in:
Matthias De Smet 2022-06-02 11:09:55 +02:00
parent 3294def3fd
commit 51be617b1c
4 changed files with 29 additions and 3 deletions
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8
modules/untar/main.nf
View file

@ -21,12 +21,18 @@ process UNTAR {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: '' def args2 = task.ext.args2 ?: ''
untar = archive.toString() - '.tar.gz' untar = archive.toString() - '.tar.gz'
""" """
mkdir output
tar \\ tar \\
-C output --strip-components 1 \\
-xzvf \\ -xzvf \\
$args \\ $args \\
$archive \\ $archive \\
$args2 \\ $args2
mv output ${untar}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

2
tests/config/test_data.config
View file

@ -323,6 +323,8 @@ params {
test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor" test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
test_flowcell = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
} }
'pacbio' { 'pacbio' {
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta" primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"

10
tests/modules/untar/main.nf
View file

@ -12,3 +12,13 @@ workflow test_untar {
UNTAR ( input ) UNTAR ( input )
} }
workflow test_untar_different_output_path {
input = [
[],
file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
]
UNTAR ( input )
}

10
tests/modules/untar/test.yml
View file

@ -1,4 +1,4 @@
- name: untar - name: untar test_untar
command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
tags: tags:
- untar - untar
@ -9,3 +9,11 @@
md5sum: a033d00cf6759407010b21700938f543 md5sum: a033d00cf6759407010b21700938f543
- path: output/untar/kraken2/taxo.k2d - path: output/untar/kraken2/taxo.k2d
md5sum: 094d5891cdccf2f1468088855c214b2c md5sum: 094d5891cdccf2f1468088855c214b2c
- name: untar test_untar_different_output_path
command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
tags:
- untar
files:
- path: output/untar/flowcell/RunInfo.xml
md5sum: 03038959f4dd181c86bc97ae71fe270a