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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
metagWGS
Commits
91a30513
Commit
91a30513
authored
Feb 25, 2021
by
Joanna Fourquet
Browse files
redirect stdout CAT to a file
parent
ac61682d
Changes
1
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main.nf
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91a30513
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@@ -1419,9 +1419,9 @@ process cat {
COUNT=`ls -1 bins/*.fa 2>/dev/null | wc -l`
if [ \$COUNT != 0 ]
then
CAT bins -b "bins/" -d database/ -t taxonomy/ -n "${task.cpus}" -s .fa --top 6 -o "${replicateId}" --I_know_what_Im_doing
CAT add_names -i "${replicateId}.ORF2LCA.txt" -o "${replicateId}.ORF2LCA.names.txt" -t taxonomy/
CAT add_names -i "${replicateId}.bin2classification.txt" -o "${replicateId}.bin2classification.names.txt" -t taxonomy/
CAT bins -b "bins/" -d database/ -t taxonomy/ -n "${task.cpus}" -s .fa --top 6 -o "${replicateId}" --I_know_what_Im_doing
> stdout_CAT.txt
CAT add_names -i "${replicateId}.ORF2LCA.txt" -o "${replicateId}.ORF2LCA.names.txt" -t taxonomy/
>> stdout_CAT.txt
CAT add_names -i "${replicateId}.bin2classification.txt" -o "${replicateId}.bin2classification.names.txt" -t taxonomy/
>> stdout_CAT.txt
else
echo "Sample ${replicateId}: no bins found, it is impossible to make taxonomic affiliation of bins."
fi
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