Merge branch 'dev' into complexity-filter-bbduk

modules.json

@@ -4,7 +4,7 @@
     "repos": {
         "nf-core/modules": {
             "adapterremoval": {
-                "git_sha": "f0800157544a82ae222931764483331a81812012"
+                "git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
             },
             "bbmap/bbduk": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

modules/nf-core/modules/adapterremoval/main.nf

@@ -12,15 +12,14 @@ process ADAPTERREMOVAL {
     path(adapterlist)
 
     output:
-    tuple val(meta), path("${prefix}.truncated.gz")            , optional: true, emit: singles_truncated
+    tuple val(meta), path("${prefix}.truncated.fastq.gz")            , optional: true, emit: singles_truncated
-    tuple val(meta), path("${prefix}.discarded.gz")            , optional: true, emit: discarded
+    tuple val(meta), path("${prefix}.discarded.fastq.gz")            , optional: true, emit: discarded
-    tuple val(meta), path("${prefix}.pair1.truncated.gz")      , optional: true, emit: pair1_truncated
+    tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz")  , optional: true, emit: paired_truncated
-    tuple val(meta), path("${prefix}.pair2.truncated.gz")      , optional: true, emit: pair2_truncated
+    tuple val(meta), path("${prefix}.collapsed.fastq.gz")            , optional: true, emit: collapsed
-    tuple val(meta), path("${prefix}.collapsed.gz")            , optional: true, emit: collapsed
+    tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz")  , optional: true, emit: collapsed_truncated
-    tuple val(meta), path("${prefix}.collapsed.truncated.gz")  , optional: true, emit: collapsed_truncated
+    tuple val(meta), path("${prefix}.paired.fastq.gz")               , optional: true, emit: paired_interleaved
-    tuple val(meta), path("${prefix}.paired.gz")               , optional: true, emit: paired_interleaved
+    tuple val(meta), path('*.settings')                              , emit: settings
-    tuple val(meta), path('*.log')                             , emit: log
+    path "versions.yml"                                              , emit: versions
-    path "versions.yml"                                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
             $adapterlist \\
             --basename ${prefix} \\
             --threads ${task.cpus} \\
-            --settings ${prefix}.log \\
             --seed 42 \\
             --gzip
 
+        ensure_fastq() {
+            if [ -f "\${1}" ]; then
+                mv "\${1}" "\${1::-3}.fastq.gz"
+            fi
+
+        }
+
+        ensure_fastq '${prefix}.truncated.gz'
+        ensure_fastq '${prefix}.discarded.gz'
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
@@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
             $adapterlist \\
             --basename ${prefix} \\
             --threads $task.cpus \\
-            --settings ${prefix}.log \\
             --seed 42 \\
             --gzip
 
+        ensure_fastq() {
+            if [ -f "\${1}" ]; then
+                mv "\${1}" "\${1::-3}.fastq.gz"
+            fi
+
+        }
+
+        ensure_fastq '${prefix}.truncated.gz'
+        ensure_fastq '${prefix}.discarded.gz'
+        ensure_fastq '${prefix}.pair1.truncated.gz'
+        ensure_fastq '${prefix}.pair2.truncated.gz'
+        ensure_fastq '${prefix}.collapsed.gz'
+        ensure_fastq '${prefix}.collapsed.truncated.gz'
+        ensure_fastq '${prefix}.paired.gz'
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")

modules/nf-core/modules/adapterremoval/meta.yml

@@ -43,43 +43,43 @@ output:
         Adapter trimmed FastQ files of either single-end reads, or singleton
         'orphaned' reads from merging of paired-end data (i.e., one of the pair
         was lost due to filtering thresholds).
-      pattern: "*.truncated.gz"
+      pattern: "*.truncated.fastq.gz"
   - discarded:
       type: file
       description: |
         Adapter trimmed FastQ files of reads that did not pass filtering
         thresholds.
-      pattern: "*.discarded.gz"
+      pattern: "*.discarded.fastq.gz"
   - pair1_truncated:
       type: file
       description: |
         Adapter trimmed R1 FastQ files of paired-end reads that did not merge
         with their respective R2 pair due to long templates. The respective pair
         is stored in 'pair2_truncated'.
-      pattern: "*.pair1.truncated.gz"
+      pattern: "*.pair1.truncated.fastq.gz"
   - pair2_truncated:
       type: file
       description: |
         Adapter trimmed R2 FastQ files of paired-end reads that did not merge
         with their respective R1 pair due to long templates. The respective pair
         is stored in 'pair1_truncated'.
-      pattern: "*.pair2.truncated.gz"
+      pattern: "*.pair2.truncated.fastq.gz"
   - collapsed:
       type: file
       description: |
         Collapsed FastQ of paired-end reads that successfully merged with their
         respective R1 pair but were not trimmed.
-      pattern: "*.collapsed.gz"
+      pattern: "*.collapsed.fastq.gz"
   - collapsed_truncated:
       type: file
       description: |
         Collapsed FastQ of paired-end reads that successfully merged with their
         respective R1 pair and were trimmed of adapter due to sufficient overlap.
-      pattern: "*.collapsed.truncated.gz"
+      pattern: "*.collapsed.truncated.fastq.gz"
   - log:
       type: file
       description: AdapterRemoval log file
-      pattern: "*.log"
+      pattern: "*.settings"
   - versions:
       type: file
       description: File containing software versions

subworkflows/local/shortread_adapterremoval.nf

@@ -5,11 +5,6 @@
 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 +31,27 @@ workflow SHORTREAD_ADAPTERREMOVAL {
 
     if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
 
-        ENSURE_FASTQ_EXTENSION1(
+        ch_concat_fastq = Channel.empty()
-            Channel.empty().mix(
+            .mix(
                 ADAPTERREMOVAL_PAIRED.out.collapsed,
                 ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
                 ADAPTERREMOVAL_PAIRED.out.singles_truncated,
-                ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
+                ADAPTERREMOVAL_PAIRED.out.paired_truncated
-                ADAPTERREMOVAL_PAIRED.out.pair2_truncated
             )
-            .map { meta, reads ->
+            .groupTuple()
-                meta.single_end = true
+            // Paired-end reads cause a nested tuple during grouping.
-                [meta, reads]
+            // We want to present a flat list of files to `CAT_FASTQ`.
-            }
+            .map { meta, fastq -> [meta, fastq.flatten()] }
-        )
 
-        CAT_FASTQ(
+        CAT_FASTQ(ch_concat_fastq)
-            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)
+            .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
 
     } else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
 
-        ENSURE_FASTQ_EXTENSION1(
+        ch_concat_fastq = Channel.empty()
-            Channel.empty().mix(
+            .mix(
                 ADAPTERREMOVAL_PAIRED.out.collapsed,
                 ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
             )
@@ -71,46 +59,17 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                 meta.single_end = true
                 [meta, reads]
             }
-        )
+            .groupTuple()
 
-        CAT_FASTQ(
+        CAT_FASTQ(ch_concat_fastq)
-            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)
+            .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
 
     } else {
 
-        ENSURE_FASTQ_EXTENSION1(
+        ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.paired_truncated
-            ADAPTERREMOVAL_PAIRED.out.pair1_truncated
+            .mix(ADAPTERREMOVAL_SINGLE.out.singles_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)
 
     }