Fix flash and cat/fastq modules (#759)

* Fix version commands: round 3

* Fix seqkit/split2 modules

* Fix flash and cat/fastq modules

* Remove md5sums on gz files

modules/cat/fastq/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,6 +23,7 @@ process CAT_FASTQ {
 
     output:
     tuple val(meta), path("*.merged.fastq.gz"), emit: reads
+    path "versions.yml"                       , emit: version
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
@@ -31,6 +32,11 @@ process CAT_FASTQ {
         if (readList.size > 1) {
             """
             cat ${readList.sort().join(' ')} > ${prefix}.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            ${getProcessName(task.process)}:
+                ${getSoftwareName(task.process)}: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
             """
         }
     } else {
@@ -41,6 +47,11 @@ process CAT_FASTQ {
             """
             cat ${read1.sort().join(' ')} > ${prefix}_1.merged.fastq.gz
             cat ${read2.sort().join(' ')} > ${prefix}_2.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            ${getProcessName(task.process)}:
+                ${getSoftwareName(task.process)}: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
             """
         }
     }

modules/flash/main.nf

@@ -21,23 +21,23 @@ process FLASH {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.merged.*.fastq.gz"), emit: reads
-    path "versions.yml"                       , emit: version
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    path "versions.yml"                , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def merged   = "-o ${prefix}.merged"
-    def input_reads = "${reads[0]} ${reads[1]}"
     """
     flash \\
         $options.args \\
-        $merged \\
+        -o ${prefix} \\
         -z \\
-        $input_reads
+        ${reads[0]} \\
+        ${reads[1]}
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(flash --version)
+        ${getSoftwareName(task.process)}: \$(echo \$(flash --version 2>&1) | sed 's/^.*FLASH v//; s/ .*\$//')
     END_VERSIONS
     """
 }

tests/modules/cat/fastq/main.nf

@@ -2,24 +2,26 @@
 
 nextflow.enable.dsl = 2
 
-include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf' addParams( options: [:] )
+include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf' addParams( options: [publish_dir:'cat'] )
 
 workflow test_cat_fastq_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
-            ]
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
+    ]
 
     CAT_FASTQ ( input )
 }
 
 workflow test_cat_fastq_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
-            ]
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
+    ]
 
     CAT_FASTQ ( input )
 }

tests/modules/cat/fastq/test.yml

@@ -4,7 +4,7 @@
     - cat
     - cat/fastq
   files:
-    - path: ./output/merged_fastq/test.merged.fastq.gz
+    - path: ./output/cat/test.merged.fastq.gz
       md5sum: 59f6dbe193741bb40f498f254aeb2e99
 
 - name: cat fastq fastqc_paired_end
@@ -13,7 +13,7 @@
     - cat
     - cat/fastq
   files:
-    - path: ./output/merged_fastq/test_2.merged.fastq.gz
+    - path: ./output/cat/test_2.merged.fastq.gz
       md5sum: d2b1a836eef1058738ecab36c907c5ba
-    - path: ./output/merged_fastq/test_1.merged.fastq.gz
+    - path: ./output/cat/test_1.merged.fastq.gz
       md5sum: 59f6dbe193741bb40f498f254aeb2e99

tests/modules/flash/main.nf

@@ -5,10 +5,11 @@ nextflow.enable.dsl = 2
 include { FLASH } from '../../../modules/flash/main.nf' addParams( options: [args:'-m 20 -M 100'] )
 
 workflow test_flash {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] 
-            ]
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
 
     FLASH ( input )
 }

tests/modules/flash/test.yml

@@ -3,9 +3,6 @@
   tags:
     - flash
   files:
-    - path: output/flash/test.merged.notCombined_2.fastq.gz
-      md5sum: 96ec044281fe60e0061976d928810314
-    - path: output/flash/test.merged.extendedFrags.fastq.gz
-      md5sum: da20afa705e8ea881e66960bb75607c9
-    - path: output/flash/test.merged.notCombined_1.fastq.gz
-      md5sum: 32451c87f89172c764bec19136592d29
+    - path: output/flash/test.notCombined_2.fastq.gz
+    - path: output/flash/test.extendedFrags.fastq.gz
+    - path: output/flash/test.notCombined_1.fastq.gz