From 0e9b2989e3fd59b6e05a77a8faf6ed89d6ddea03 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 5 Apr 2022 10:53:04 +0200
Subject: [PATCH] refactor: remove superfluous ENSURE_FASTQ_EXTENSION

---
 .../local/shortread_adapterremoval.nf         | 75 ++++---------------
 1 file changed, 16 insertions(+), 59 deletions(-)

diff --git a/subworkflows/local/shortread_adapterremoval.nf b/subworkflows/local/shortread_adapterremoval.nf
index e522a1a..8c02f6f 100644
--- a/subworkflows/local/shortread_adapterremoval.nf
+++ b/subworkflows/local/shortread_adapterremoval.nf
@@ -5,11 +5,6 @@ Process short raw reads with AdapterRemoval
 include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE       } from '../../modules/nf-core/modules/adapterremoval/main'
 include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED       } from '../../modules/nf-core/modules/adapterremoval/main'
 include { CAT_FASTQ                                     } from '../../modules/nf-core/modules/cat/fastq/main'
-include {
-    ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION1;
-    ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION2;
-    ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION3;
-} from '../../modules/local/ensure_fastq_extension'
 
 workflow SHORTREAD_ADAPTERREMOVAL {
 
@@ -36,34 +31,25 @@ workflow SHORTREAD_ADAPTERREMOVAL {
 
     if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
 
-        ENSURE_FASTQ_EXTENSION1(
-            Channel.empty().mix(
+        ch_concat_fastq = Channel.empty()
+            .mix(
                 ADAPTERREMOVAL_PAIRED.out.collapsed,
                 ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
                 ADAPTERREMOVAL_PAIRED.out.singles_truncated,
-                ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
-                ADAPTERREMOVAL_PAIRED.out.pair2_truncated
+                ADAPTERREMOVAL_PAIRED.out.paired_truncated
             )
-            .map { meta, reads ->
-                meta.single_end = true
-                [meta, reads]
-            }
-        )
+            .groupTuple()
+            .map { [it.head(), it.tail().flatten()] }
 
-        CAT_FASTQ(
-            ENSURE_FASTQ_EXTENSION1.out.reads
-                .groupTuple()
-        )
-
-        ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
+        CAT_FASTQ(ch_concat_fastq)
 
         ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
-            .mix(ENSURE_FASTQ_EXTENSION2.out.reads)
+            .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
 
     } else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
 
-        ENSURE_FASTQ_EXTENSION1(
-            Channel.empty().mix(
+        ch_concat_fastq = Channel.empty()
+            .mix(
                 ADAPTERREMOVAL_PAIRED.out.collapsed,
                 ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
             )
@@ -71,54 +57,25 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                 meta.single_end = true
                 [meta, reads]
             }
-        )
+            .groupTuple()
 
-        CAT_FASTQ(
-            ENSURE_FASTQ_EXTENSION1.out.reads
-                .groupTuple()
-        )
-
-        ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
+        CAT_FASTQ(ch_concat_fastq)
 
         ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
-            .mix(ENSURE_FASTQ_EXTENSION2.out.reads)
+            .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
 
     } else {
 
-        ENSURE_FASTQ_EXTENSION1(
-            ADAPTERREMOVAL_PAIRED.out.pair1_truncated
-            .map { meta, reads ->
-                meta.single_end = true
-                [meta, reads]
-            }
-        )
-
-        ENSURE_FASTQ_EXTENSION2(
-            ADAPTERREMOVAL_PAIRED.out.pair2_truncated
-            .map { meta, reads ->
-                meta.single_end = true
-                [meta, reads]
-            }
-        )
-
-        ENSURE_FASTQ_EXTENSION3(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
-
-        ch_adapterremoval_reads_prepped = ENSURE_FASTQ_EXTENSION1.out.reads
-            .join(ENSURE_FASTQ_EXTENSION2.out.reads)
-            .groupTuple()
-            .map { meta, pair1, pair2 ->
-                meta.single_end = false
-                [ meta, [ pair1, pair2 ].flatten() ]
-            }
-            .mix(ENSURE_FASTQ_EXTENSION3.out.reads)
+        ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.paired_truncated
+            .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
 
     }
 
     ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
     ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
     ch_multiqc_files = ch_multiqc_files.mix(
-        ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]},
-        ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]}
+        ADAPTERREMOVAL_PAIRED.out.settings.collect{it[1]},
+        ADAPTERREMOVAL_SINGLE.out.settings.collect{it[1]}
     )
 
     emit: