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bwameth/align: fix fasta name retrieval

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apparently bwameth doesn't like './' in front of the filepath? I have no idea. This works however
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phue 2021-02-20 13:12:43 +01:00
parent 2d8baa8b75
commit bf0e0d857d
1 changed files with 1 additions and 1 deletions
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software/bwameth/align/main.nf
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@ -31,7 +31,7 @@ process BWAMETH_ALIGN {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
"""
INDEX=`find -L ./ -name "*bwameth.c2t" | sed 's/.bwameth.c2t//'`
INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'`
bwameth.py \\
$options.args \\