Support gzipped genome in gem index process

guigolab · Oct 6, 2022 · 87bbbe8 · 87bbbe8
1 parent aeed44e
commit 87bbbe8
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/modules/gem.nf b/modules/gem.nf
@@ -6,8 +6,9 @@ process indexing {
     file "genome_index.gem"
 
     script:
+    def cat = genome.name.endsWith('.gz') ? 'zcat' : 'cat'
     """
-    sed 's/ .*//' ${genome} > genome_processed.fa
+    ${cat} ${genome} | sed 's/ .*//' > genome_processed.fa
     gem-indexer -i genome_processed.fa \
                 -o genome_index \
                 -T ${task.cpus} \