Commit 5cb7cfb2 authored by Valentina Galata's avatar Valentina Galata
Browse files

issue #38: redirect echo in if-clause to stderr [ci skip]

parent 35a37a90
Pipeline #45805 skipped
# NOTE: based on code from XXX
# https://github.com/lmrodriguezr/nonpareil
# does not support gzipped FASTQ files: https://github.com/lmrodriguezr/nonpareil/issues/35
# NOTE: the tool does not support gzipped FASTQ files: https://github.com/lmrodriguezr/nonpareil/issues/35
rule nonpareil:
input:
'Preprocessing/mg.{read}.preprocessed.fq'
......@@ -26,11 +25,11 @@ rule nonpareil:
"""
bname={output.out[0]}
if [ {params.minlen} -ge 24 ]; then
echo "reads >= 24"
>&2 echo "all reads >= 24 - linking to input file"
ln -s $(realpath {input}) {output.fq}
else
echo "rm reads < 24"
seqkit seq {input} -j {threads} -m 24 | zcat > {output.fq}
>&2 echo "remove reads < 24"
seqkit seq {input} -j {threads} -m 24 > {output.fq}
fi 2> {log}
nonpareil -s {output.fq} -T kmer -f fastq -b ${{bname%.*}} &>> {log}
"""
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment