samtools and picardtools: add compatibility with mutliqc

src/nf_modules/picard/main.nf

@@ -15,7 +15,7 @@ process mark_duplicate {
     tuple val(file_id), path(bam)
   output:
     tuple val(file_id) , path("*.bam"), emit: bam
-    path "*_report.txt", emit: report
+    path "*_report.dupinfo.txt", emit: report
 
 
   script:
@@ -24,7 +24,7 @@ PicardCommandLine MarkDuplicates \
   ${params.mark_duplicate} \
   INPUT=${bam} \
   OUTPUT=${bam.baseName}_dedup.bam \
-  METRICS_FILE=${bam.baseName}_picard_dedup_report.txt &> \
+  METRICS_FILE=${bam.baseName}_picard_dedup_report.dupinfo.txt &> \
   picard_${bam.baseName}.log
 """
 }

src/nf_modules/samtools/main.nf

@@ -270,9 +270,11 @@ process stats_bam {
 
   output:
     tuple val(file_id), path("*.tsv"), emit: tsv
+    tuple val(file_id), path("*.flagstat.txt"), emit: report 
   script:
 """
 samtools flagstat -@ ${task.cpus} ${params.stats_bam} -O tsv ${bam} > ${bam.simpleName}.flagstat.txt
+cp ${bam.simpleName}.flagstat.txt ${bam.simpleName}.tsv
 """
 }