Fix the parser to integrate sourmash properly

RVanDamme · Nov 24, 2020 · ea5e452 · ea5e452
1 parent 8ee842c
commit ea5e452
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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
     """
-}
+}