diff --git a/modules/checkm_sourmash_parser.nf b/modules/checkm_sourmash_parser.nf index 4bbab4a..2a0dfff 100644 --- a/modules/checkm_sourmash_parser.nf +++ b/modules/checkm_sourmash_parser.nf @@ -12,7 +12,7 @@ process sourmash_checkm_parser { shell: """ grep -v "] INFO: " !{checkm} | grep -v "\\-\\-\\-\\-\\-\\-\\-" | grep -v "Bin Id" | sed -e 's/^[ \\t]*//'|sed 's/[ \\t]*\$//' |sed -r 's/ +/,/g'|sed '/^\$/d' >checkm.csv - for file in ${sourmash}; do tail -n 1 \$file | sed -e 's/.fa//' >>sourmash.csv; done + for file in \$(ls bin*.txt); do tail -n 1 \$file | sed -e 's/.fa//' >>sourmash.csv; done checkm_sourmash_parser.py -c checkm.csv -s sourmash.csv """ -} \ No newline at end of file +}