fix: insert .fastq file extension

The MetaPhlAn3 module computes the input type from the file extension
without the possibility to configure an override. Since AdapterRemoval2
creates files without `.fastq` extensions, MetaPhlAn3 input was determined
to be SAM.

modules/local/ensure_fastq_extension.nf

@@ -0,0 +1,31 @@
+process ENSURE_FASTQ_EXTENSION {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "conda-forge::bash=5.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
+        'biocontainers/biocontainers:v1.2.0_cv2' }"
+
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path('*.fastq.gz'), emit: reads
+
+    script:
+    if (meta.single_end) {
+        fastq = "${reads.baseName}.fastq.gz"
+        """
+        ln -s '${reads}' '${fastq}'
+        """
+    } else {
+        first = "${reads[0].baseName}.fastq.gz"
+        second = "${reads[1].baseName}.fastq.gz"
+        """
+        ln -s '${reads[0]}' '${first}'
+        ln -s '${reads[1]}' '${second}'
+        """
+    }
+}

subworkflows/local/shortread_adapterremoval.nf

@@ -5,6 +5,11 @@ 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 {
 
@@ -30,59 +35,102 @@ workflow SHORTREAD_ADAPTERREMOVAL {
      */
 
     if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
-        ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
-                                                .mix(
-                                                    ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
-                                                    ADAPTERREMOVAL_PAIRED.out.singles_truncated,
-                                                    ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
-                                                    ADAPTERREMOVAL_PAIRED.out.pair2_truncated
-                                                    )
-                                                .map {
-                                                    meta, reads ->
-                                                        def meta_new = meta.clone()
-                                                        meta_new.single_end = true
 
-                                                        [ meta_new, reads ]
+        ENSURE_FASTQ_EXTENSION1(
-                                                    }
+            Channel.empty().mix(
-                                                    .groupTuple()
+                ADAPTERREMOVAL_PAIRED.out.collapsed,
+                ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
+                ADAPTERREMOVAL_PAIRED.out.singles_truncated,
+                ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
+                ADAPTERREMOVAL_PAIRED.out.pair2_truncated
+            )
+            .map { meta, reads ->
+                meta.single_end = true
+                [meta, reads]
+            }
+        )
 
-        ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
+        CAT_FASTQ(
-                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
+            ENSURE_FASTQ_EXTENSION1.out.reads
+                .groupTuple()
+        )
+
+        ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
+
+        ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
+            .mix(ENSURE_FASTQ_EXTENSION2.out.reads)
 
     } else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
-        ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
-                                                .mix( ADAPTERREMOVAL_PAIRED.out.collapsed_truncated )
-                                                .map {
-                                                    meta, reads ->
-                                                        def meta_new = meta.clone()
-                                                        meta_new['single_end'] = true
 
-                                                        [ meta_new, reads ]
+        ENSURE_FASTQ_EXTENSION1(
-                                                    }
+            Channel.empty().mix(
-                                                    .groupTuple(by: 0)
+                ADAPTERREMOVAL_PAIRED.out.collapsed,
+                ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
+            )
+            .map { meta, reads ->
+                meta.single_end = true
+                [meta, reads]
+            }
+        )
 
-        ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
+        CAT_FASTQ(
-                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
+            ENSURE_FASTQ_EXTENSION1.out.reads
+                .groupTuple()
+        )
+
+        ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
+
+        ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
+            .mix(ENSURE_FASTQ_EXTENSION2.out.reads)
 
     } else {
 
-        ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.pair1_truncated
+        ENSURE_FASTQ_EXTENSION1(
-                                                .join( ADAPTERREMOVAL_PAIRED.out.pair2_truncated )
+            ADAPTERREMOVAL_PAIRED.out.pair1_truncated
-                                                .groupTuple()
+            .map { meta, reads ->
-                                                .map { meta, pair1, pair2 ->
+                meta.single_end = true
-                                                        [ meta, [ pair1, pair2 ].flatten() ]
+                [meta, reads]
-                                                }
+            }
-                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
+        )
-    }
 
-    ch_processed_reads = ch_adapterremoval_reads_prepped
+        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_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]} )
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]},
+        ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]}
+    )
 
     emit:
-    reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]
+    reads    = ch_adapterremoval_reads_prepped  // channel: [ val(meta), [ reads ] ]
-    versions = ch_versions          // channel: [ versions.yml ]
+    versions = ch_versions  // channel: [ versions.yml ]
     mqc      = ch_multiqc_files
 }
+
+def ensureFastQExtension(row) {
+    def (meta, read) = row
+    def filename = file(read.parent).resolve("${read.baseName}.fastq.gz")
+
+    read.renameTo(filename.toString())
+    return [meta, read]
+}