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Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
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Maxime U. Garcia 2022-06-08 11:38:02 +02:00 committed by GitHub
parent 7230bf2174
commit 4935bb98cb
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1 changed files with 2 additions and 2 deletions
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modules/tiddit/sv/main.nf
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@ -8,7 +8,7 @@ process TIDDIT_SV {
'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }" 'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
input: input:
tuple val(meta), path(input), path(index) tuple val(meta), path(input), path(input_index)
path fasta path fasta
path bwa_index path bwa_index
@ -24,7 +24,7 @@ process TIDDIT_SV {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
[[ -d $bwa_index ]] && for i in `ls $bwa_index`; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s $bwa_index/\$i ${fasta}.\${i##*.} || ln -s $bwa_index/\$i \$i; done [[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s $bwa_index/\$i ${fasta}.\${i##*.} || ln -s $bwa_index/\$i \$i; done
tiddit \\ tiddit \\
--sv \\ --sv \\