millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

cover all use cases

Browse source
This commit is contained in:
MaxUlysse 2022-06-03 15:37:10 +02:00
parent f1a5cc07db
commit f9ac4e28e9
1 changed files with 1 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

6
modules/tiddit/sv/main.nf
View file

@ -26,11 +26,7 @@ process TIDDIT_SV {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--ref $fasta" : "" def reference = fasta ? "--ref $fasta" : ""
""" """
for i in `ls ${bwa_index}` [[ -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
do
ln -s ${bwa_index}/\$i ${fasta}.\${i##*.}
done
tiddit \\ tiddit \\
--sv \\ --sv \\