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fix bgziptabix extension (#1784)

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* fix bgziptabix extension

* update test.yml
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nvnieuwk 2022-06-15 10:33:10 +02:00 committed by GitHub
parent 0af6adef55
commit 9dbaffff88
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2 changed files with 6 additions and 6 deletions
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4
modules/tabix/bgziptabix/main.nf
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@ -22,8 +22,8 @@ process TABIX_BGZIPTABIX {
def args2 = task.ext.args2 ?: '' def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
bgzip --threads ${task.cpus} -c $args $input > ${prefix}.gz bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
tabix $args2 ${prefix}.gz tabix $args2 ${prefix}.${input.getExtension()}.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

8
tests/modules/tabix/bgziptabix/test.yml
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@ -1,10 +1,10 @@
- name: tabix bgziptabix - name: tabix bgziptabix test_tabix_bgziptabix
command: nextflow run ./tests/modules/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgziptabix/nextflow.config command: nextflow run ./tests/modules/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgziptabix/nextflow.config
tags: tags:
- tabix
- tabix/bgziptabix - tabix/bgziptabix
- tabix
files: files:
- path: ./output/tabix/test.gz - path: output/tabix/test.vcf.gz
md5sum: fc178eb342a91dc0d1d568601ad8f8e2 md5sum: fc178eb342a91dc0d1d568601ad8f8e2
- path: ./output/tabix/test.gz.tbi - path: output/tabix/test.vcf.gz.tbi
md5sum: 36e11bf96ed0af4a92caa91a68612d64 md5sum: 36e11bf96ed0af4a92caa91a68612d64