fix

ghga-de · Jan 23, 2024 · f0d8318 · f0d8318
1 parent b071224
commit f0d8318
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/modules/local/cluster_segments.nf b/modules/local/cluster_segments.nf
@@ -43,7 +43,8 @@ process CLUSTER_SEGMENTS {
         --sex $sexfile \\
         --gcCovWidthFile  $gc_corrected \\
         --chrLengthFile   $chrlenght \\
-        --pid   ${prefix}
+        --pid   ${prefix} \\
+        $args
 
     # Not sure why there is a NULL line in the end of the segments file
     zcat ${prefix}_all_seg2.txt.gz  | grep -v NULL | bgzip -f > ${prefix}_all_seg_2.txt.gz.2

diff --git a/modules/local/merge_snp.nf b/modules/local/merge_snp.nf
@@ -19,7 +19,7 @@ process MERGE_SNP {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def snp_min_coverage = meta.iscontrol == "" ? "${params.snp_min_coverage}" : "0"
+    def snp_min_coverage = meta.iscontrol == "1" ? "${params.snp_min_coverage}" : "0"
 
     """
     merge_and_filter_snp.py \\