Accept RefSeq accession numbers and remove plasmids

oist · Nov 20, 2024 · b0c0c18 · b0c0c18
1 parent b6c7fb3
commit b0c0c18
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/modules/local/filter.nf b/modules/local/filter.nf
@@ -37,11 +37,11 @@ process FILTER {
     # - does that assembly has sex chromosomes?
     cut -c 1-2 ${prefix}.orig_bgzipped.fa.fai | sort | uniq -c | sort -n > ${prefix}.patterns.txt
 
-    # Keep only complete chromosomes but remove the mitogenome
+    # Keep only complete chromosomes but remove the mitogenome and plasmids
     sed 's/^>//' ${prefix}.contignames.txt |
-        grep -vi mitochondri |
+        grep -vi -e mitochondri -e plasmid |
         awk '{print \$1}' |
-        grep -E "^(CM|CP|FR|L[R-T]|O[U-Z])" > ${prefix}.contignames.chromosomes.txt ||
+        grep -E "^(CM|CP|FR|L[R-T]|NC|NZ|O[U-Z])" > ${prefix}.contignames.chromosomes.txt ||
         true > /dev/null # Returns success even if list is empty.
     samtools faidx -r ${prefix}.contignames.chromosomes.txt ${prefix}.orig_bgzipped.fa.gz | bgzip --threads $task.cpus --compress-level 9 > ${prefix}.chromosomes.fa.gz