mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
fix untar output dir
This commit is contained in:
parent
3294def3fd
commit
51be617b1c
4 changed files with 29 additions and 3 deletions
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@ -21,12 +21,18 @@ process UNTAR {
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def args2 = task.ext.args2 ?: ''
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untar = archive.toString() - '.tar.gz'
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untar = archive.toString() - '.tar.gz'
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"""
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"""
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mkdir output
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tar \\
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tar \\
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-C output --strip-components 1 \\
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-xzvf \\
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-xzvf \\
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$args \\
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$args \\
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$archive \\
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$archive \\
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$args2 \\
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$args2
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mv output ${untar}
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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@ -323,6 +323,8 @@ params {
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test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
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test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
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test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
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test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
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test_flowcell = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
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}
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}
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'pacbio' {
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'pacbio' {
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primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
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primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
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@ -12,3 +12,13 @@ workflow test_untar {
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UNTAR ( input )
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UNTAR ( input )
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}
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}
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workflow test_untar_different_output_path {
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input = [
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[],
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file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
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]
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UNTAR ( input )
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}
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@ -1,4 +1,4 @@
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- name: untar
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- name: untar test_untar
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command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
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command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
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tags:
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tags:
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- untar
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- untar
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@ -9,3 +9,11 @@
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md5sum: a033d00cf6759407010b21700938f543
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md5sum: a033d00cf6759407010b21700938f543
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- path: output/untar/kraken2/taxo.k2d
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- path: output/untar/kraken2/taxo.k2d
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md5sum: 094d5891cdccf2f1468088855c214b2c
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md5sum: 094d5891cdccf2f1468088855c214b2c
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- name: untar test_untar_different_output_path
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command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
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tags:
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- untar
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files:
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- path: output/untar/flowcell/RunInfo.xml
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md5sum: 03038959f4dd181c86bc97ae71fe270a
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