made adapters channel instead of meta

nf-core · Oct 25, 2024 · e963569 · e963569
1 parent 694ab44
commit e963569
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Showing 3 changed files with 22 additions and 25 deletions.
diff --git a/modules/nf-core/cutadapt/cutadapt.diff b/modules/nf-core/cutadapt/cutadapt.diff
diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
@@ -577,27 +577,17 @@ workflow ILLUMINA {
     //
     ch_cutadapt_multiqc = Channel.empty()
     if (params.protocol == 'amplicon' && !params.skip_assembly && !params.skip_cutadapt) {
+        ch_primers =  PREPARE_GENOME.out.primer_fasta.collect { it[1] }
         if (!params.skip_noninternal_primers){
             PREPARE_PRIMER_FASTA(
                 PREPARE_GENOME.out.primer_fasta.collect { it[1] }
                 )
-            ch_assembly_fastq
-                .map { info, reads ->
-                    def meta = info +
-                        [primers: PREPARE_PRIMER_FASTA.out.adapters.value]
-                    return [meta, reads] }
-                .set{ ch_assembly_fastq }
-        } else {
-            ch_assembly_fastq
-                .map { info, reads ->
-                    def meta = info +
-                        [primers: PREPARE_GENOME.out.primer_fasta.value[1]]
-                    return [meta, reads] }
-                .set{ ch_assembly_fastq }
+            ch_primers = PREPARE_PRIMER_FASTA.out.adapters
         }
 
         CUTADAPT (
-            ch_assembly_fastq
+            ch_assembly_fastq,
+            ch_primers
         )
         ch_assembly_fastq   = CUTADAPT.out.reads
         ch_cutadapt_multiqc = CUTADAPT.out.log