Merge pull request #108 from rki-mf1/fix-bbduk-after-summary-PR

fix bbduk which has no bam channel for the new summary script

clean.nf

@@ -181,7 +181,6 @@ lib_pairedness = params.input_type == 'illumina' ? 'paired' : 'single'
 
 include { prepare_contamination } from './workflows/prepare_contamination_wf' addParams( tool: tool )
 include { check_own as prepare_keep } from './modules/prepare_contamination'
-
 include { clean } from './workflows/clean_wf' addParams( tool: tool, lib_pairedness: lib_pairedness )
 include { keep } from './workflows/keep_wf' addParams( tool: tool, lib_pairedness: lib_pairedness )
 include { summarize } from './workflows/summarize_wf'
@@ -196,13 +195,10 @@ workflow {
   contamination = prepare_contamination.out
 
   clean(input_ch, contamination, nanoControlBedChannel, 'map-to-remove')
-
-  bam_sort = clean.out.sort_bam_ch
-
+
   if (!params.bbduk) {
-
-      summarize(bam_sort)
-
+    bam_sort = clean.out.sort_bam_ch
+    summarize(bam_sort)
   }
 
   if (params.keep){

workflows/clean_wf.nf

@@ -21,6 +21,7 @@ workflow clean {
             flagstats = Channel.empty()
             out_reads = bbduk.out.cleaned_reads.concat(bbduk.out.contaminated_reads)
             bams_bai = Channel.empty()
+            sort_bam_ch = Channel.empty()
         } 
         else {
             minimap2(input, contamination) | sort_bam | index_bam | ( idxstats_from_bam & flagstats_from_bam )
@@ -50,7 +51,7 @@ workflow clean {
             idxstats = idxstats_from_bam.out
             flagstats = flagstats_from_bam.out
             out_reads = fastq_from_bam.out
-	    sort_bam_ch = sort_bam.out
+	        sort_bam_ch = sort_bam.out
         }
 
     emit:
@@ -59,5 +60,5 @@ workflow clean {
         flagstats
         out_reads
         bams_bai
-	sort_bam_ch
+	    sort_bam_ch
 }