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Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java

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This commit is contained in:
Nicolas Vannieuwkerke 2022-04-28 14:29:39 +02:00
commit c6ea41948d
3 changed files with 4 additions and 2 deletions
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2
modules/gatk4/haplotypecaller/main.nf
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@ -17,7 +17,7 @@ process GATK4_HAPLOTYPECALLER {
output: output:
tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.vcf.gz"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*.tbi") , optional:true, emit: tbi
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:

2
modules/tiddit/sv/main.nf
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@ -24,7 +24,7 @@ process TIDDIT_SV {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : "" def reference = fasta ? "--ref $fasta" : ""
""" """
tiddit \\ tiddit \\
--sv \\ --sv \\

2
tests/modules/tiddit/sv/test.yml
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@ -9,6 +9,7 @@
- path: output/tiddit/test.signals.tab - path: output/tiddit/test.signals.tab
md5sum: dab4b2fec4ddf8eb1c23005b0770150e md5sum: dab4b2fec4ddf8eb1c23005b0770150e
- path: output/tiddit/test.vcf - path: output/tiddit/test.vcf
md5sum: bdce14ae8292bf3deb81f6f255baf859
- name: tiddit sv no ref - name: tiddit sv no ref
command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
@ -21,3 +22,4 @@
- path: output/tiddit/test.signals.tab - path: output/tiddit/test.signals.tab
md5sum: dab4b2fec4ddf8eb1c23005b0770150e md5sum: dab4b2fec4ddf8eb1c23005b0770150e
- path: output/tiddit/test.vcf - path: output/tiddit/test.vcf
md5sum: 3d0e83a8199b2bdb81cfe3e6b12bf64b