Refactor adapterremoval (#1491)

* refactor: insert .fastq file extensions

* style: insert whitespace

* refactor: create paired output

* refactor: rename settings from log

Requested by @jfy133

* tests: correct expected output

* fix: remove settings option due to default

* chore: rename output patterns

* refactor: omit paired files in single-end

* refactor: rename output to settings

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/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

tests/modules/adapterremoval/test.yml

@@ -3,10 +3,10 @@
   tags:
     - adapterremoval
   files:
-    - path: output/adapterremoval/test.discarded.gz
+    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.log
+    - path: output/adapterremoval/test.settings
       md5sum: 2fd3d5d703b63ba33a83021fccf25f77
-    - path: output/adapterremoval/test.truncated.gz
+    - path: output/adapterremoval/test.truncated.fastq.gz
       md5sum: 62139afee94defad5b83bdd0b8475a1f
     - path: output/adapterremoval/versions.yml
       md5sum: ac5b46719719b7ee62739530b80869fc
@@ -16,12 +16,12 @@
   tags:
     - adapterremoval
   files:
-    - path: output/adapterremoval/test.discarded.gz
+    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.log
+    - path: output/adapterremoval/test.settings
       md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
-    - path: output/adapterremoval/test.pair1.truncated.gz
+    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
       md5sum: 294a6277f0139bd597e57c6fa31f39c7
-    - path: output/adapterremoval/test.pair2.truncated.gz
+    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
       md5sum: de7b38e2c881bced8671acb1ab452d78
     - path: output/adapterremoval/versions.yml
       md5sum: fa621c887897da5a379c719399c17db7
@@ -31,15 +31,15 @@
   tags:
     - adapterremoval
   files:
-    - path: output/adapterremoval/test.collapsed.gz
+    - path: output/adapterremoval/test.collapsed.fastq.gz
       md5sum: ff956de3532599a56c3efe5369f0953f
-    - path: output/adapterremoval/test.collapsed.truncated.gz
+    - path: output/adapterremoval/test.collapsed.truncated.fastq.gz
-    - path: output/adapterremoval/test.discarded.gz
+    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.log
+    - path: output/adapterremoval/test.settings
       md5sum: 7f0b2328152226e46101a535cce718b3
-    - path: output/adapterremoval/test.pair1.truncated.gz
+    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
       md5sum: 683be19bc1c83008944b6b719bfa34e1
-    - path: output/adapterremoval/test.pair2.truncated.gz
+    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
       md5sum: e6548fe061f3ef86368b26da930174d0
     - path: output/adapterremoval/versions.yml
       md5sum: 78f589bb313c8da0147ca8ce77d7f3bf