add samplegender from sex_check

nf-core · Nov 15, 2024 · 73e8505 · 73e8505
1 parent 85c1277
commit 73e8505
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -903,7 +903,7 @@ workflow RAREDISEASE {
 
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(NGSBITS_SAMPLEGENDER.out.tsv.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([]))