Commit 91a30513 authored by Joanna Fourquet's avatar Joanna Fourquet
Browse files

redirect stdout CAT to a file

parent ac61682d
...@@ -1419,9 +1419,9 @@ process cat { ...@@ -1419,9 +1419,9 @@ process cat {
COUNT=`ls -1 bins/*.fa 2>/dev/null | wc -l` COUNT=`ls -1 bins/*.fa 2>/dev/null | wc -l`
if [ \$COUNT != 0 ] if [ \$COUNT != 0 ]
then then
CAT bins -b "bins/" -d database/ -t taxonomy/ -n "${task.cpus}" -s .fa --top 6 -o "${replicateId}" --I_know_what_Im_doing 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/ 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/ CAT add_names -i "${replicateId}.bin2classification.txt" -o "${replicateId}.bin2classification.names.txt" -t taxonomy/ >> stdout_CAT.txt
else else
echo "Sample ${replicateId}: no bins found, it is impossible to make taxonomic affiliation of bins." echo "Sample ${replicateId}: no bins found, it is impossible to make taxonomic affiliation of bins."
fi fi
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