Commit d4752507 authored by Valentina Galata's avatar Valentina Galata
Browse files

issue #33: tmp dirs for work dirs in sortmerna rule [ci skip]

parent 1a04b542
Pipeline #45809 skipped
......@@ -60,26 +60,24 @@ rule filter_rna:
"filter_rna: filtering rRNA from mt reads."
# NOTE: sub-folder kvdb/ in the work directory has to be cleaned before running sortmerna
if [ -d {TMPDIR}/kvdb ]; then
rm -Rf {TMPDIR}/kvdb
TMPDIR_PE=$(mktemp -d -p {TMPDIR})
TMPDIR_SE=$(mktemp -d -p {TMPDIR})
sortmerna {params.ref} {params.params} {params.params_pe} --threads {threads} \
--reads {input.r1} --reads {input.r2} --workdir {TMPDIR} --aligned {params.bname_pe_rrna} --other {params.bname_pe_filt} &> {log}
--reads {input.r1} --reads {input.r2} --workdir ${{TMPDIR_PE}} --aligned {params.bname_pe_rrna} --other {params.bname_pe_filt} &> {log}
rsync -tPv {output.tmp_filt_r1} {output.filt_r1} &>> {log}
rsync -tPv {output.tmp_filt_r2} {output.filt_r2} &>> {log}
rsync -tPv {output.tmp_rrna_r1} {output.rrna_r1} &>> {log}
rsync -tPv {output.tmp_rrna_r2} {output.rrna_r2} &>> {log}
if [ ! -s {output.otu} ]; then
if [ ! -s {output.otu} ]; then # empty or does not exist
touch {output.otu}
echo "# WARNING: OTU from sortmerna file does not exists" > status/sortmerna.warning
rm -f {TMPDIR}/kvdb/*
sortmerna {params.ref} {params.params} --threads {threads} \
--reads {} --workdir {TMPDIR} --aligned {params.bname_se_rrna} --other {params.bname_se_filt} &>> {log}
--reads {} --workdir ${{TMPDIR_SE}} --aligned {params.bname_se_rrna} --other {params.bname_se_filt} &>> {log}
cat {params.bname_pe_rrna}.log {params.bname_se_rrna}.log >> {log} && rm {params.bname_pe_rrna}.log {params.bname_se_rrna}.log
rm -rf ${{TMPDIR_PE}} ${{TMPDIR_SE}}
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