From e963569d87f4bb0e9d733a166aa3b62c72a7a32a Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Fri, 25 Oct 2024 16:13:17 +0200
Subject: [PATCH] made adapters channel instead of meta

---
 modules/nf-core/cutadapt/cutadapt.diff | 19 +++++++++++++------
 modules/nf-core/cutadapt/main.nf       | 10 +++++-----
 workflows/illumina.nf                  | 18 ++++--------------
 3 files changed, 22 insertions(+), 25 deletions(-)

diff --git a/modules/nf-core/cutadapt/cutadapt.diff b/modules/nf-core/cutadapt/cutadapt.diff
index fcbff0f2..2a450c54 100644
--- a/modules/nf-core/cutadapt/cutadapt.diff
+++ b/modules/nf-core/cutadapt/cutadapt.diff
@@ -3,22 +3,29 @@ Changes in module 'nf-core/cutadapt'
 Changes in 'cutadapt/main.nf':
 --- modules/nf-core/cutadapt/main.nf
 +++ modules/nf-core/cutadapt/main.nf
-@@ -22,11 +22,26 @@
+@@ -9,6 +9,7 @@
+ 
+     input:
+     tuple val(meta), path(reads)
++    path adapters
+ 
+     output:
+     tuple val(meta), path('*.trim.fastq.gz'), emit: reads
+@@ -22,11 +23,25 @@
      def args = task.ext.args ?: ''
      def prefix = task.ext.prefix ?: "${meta.id}"
      def trimmed  = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
-+    def threeprime_adapters = params.threeprime_adapters ?: false
 +
 +    // Ajustar primers según las condiciones dadas
 +    def primers
 +    if (params.threeprime_adapters && meta.single_end) {
-+        primers = "-a file:${meta.primers}"
++        primers = "-a file:${adapters}"
 +    } else if (params.threeprime_adapters && !meta.single_end) {
-+        primers = "-a file:${meta.primers} -A file:${meta.primers}"
++        primers = "-a file:${adapters} -A file:${adapters}"
 +    } else if (!params.threeprime_adapters && meta.single_end) {
-+        primers = "-g file:${meta.primers}"
++        primers = "-g file:${adapters}"
 +    } else {
-+        primers = "-g file:${meta.primers} -G file:${meta.primers}"
++        primers = "-g file:${adapters} -G file:${adapters}"
 +    }
 +    
      """
diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf
index 2a1f92c6..01ff1173 100644
--- a/modules/nf-core/cutadapt/main.nf
+++ b/modules/nf-core/cutadapt/main.nf
@@ -9,6 +9,7 @@ process CUTADAPT {
 
     input:
     tuple val(meta), path(reads)
+    path adapters
 
     output:
     tuple val(meta), path('*.trim.fastq.gz'), emit: reads
@@ -22,18 +23,17 @@ process CUTADAPT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def trimmed  = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
-    def threeprime_adapters = params.threeprime_adapters ?: false
 
     // Ajustar primers según las condiciones dadas
     def primers
     if (params.threeprime_adapters && meta.single_end) {
-        primers = "-a file:${meta.primers}"
+        primers = "-a file:${adapters}"
     } else if (params.threeprime_adapters && !meta.single_end) {
-        primers = "-a file:${meta.primers} -A file:${meta.primers}"
+        primers = "-a file:${adapters} -A file:${adapters}"
     } else if (!params.threeprime_adapters && meta.single_end) {
-        primers = "-g file:${meta.primers}"
+        primers = "-g file:${adapters}"
     } else {
-        primers = "-g file:${meta.primers} -G file:${meta.primers}"
+        primers = "-g file:${adapters} -G file:${adapters}"
     }
     
     """
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
index 75da7b31..668e7c09 100644
--- 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