CAT: Use meta map and supply output file name via modules.config (#1446)

* Use meta map and supply output file name via modules.config

* Remove all def declarations to make it work

* update tests & remove extra .

* fix ze tests

* update meta.yml with meta map info

* add tag line now that meta is available

modules/cat/cat/main.nf

@@ -1,4 +1,5 @@
 process CAT_CAT {
+    tag "$meta.id"
     label 'process_low'
 
     conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null)
@@ -7,12 +8,11 @@ process CAT_CAT {
         'quay.io/biocontainers/pigz:2.3.4' }"
 
     input:
-    path files_in
+    tuple val(meta), path(files_in)
-    val  file_out
 
     output:
-    path "${file_out}*" , emit: file_out
+    tuple val(meta), path("${prefix}"), emit: file_out
-    path "versions.yml" , emit: versions
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,16 +29,18 @@ process CAT_CAT {
     // | gzipped   | ungzipped  | zcat     |          |
     // | ungzipped | gzipped    | cat      | pigz     |
 
-    def in_zip   = file_list[0].endsWith('.gz')
+    // Use input file ending as default
-    def out_zip  = file_out.endsWith('.gz')
+    prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
-    def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
+    out_zip  = prefix.endsWith('.gz')
-    def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
+    in_zip   = file_list[0].endsWith('.gz')
+    command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
+    command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
     """
     $command1 \\
         $args \\
         ${file_list.join(' ')} \\
         $command2 \\
-        > $file_out
+        > ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/cat/cat/meta.yml

@@ -12,13 +12,15 @@ tools:
       tool_dev_url: None
       licence: ["GPL-3.0-or-later"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - files_in:
       type: file
       description: List of compressed / uncompressed files
       pattern: "*"
-  - file_out:
-      type: value
-      description: Full name of output file with or without .gz extension
 
 output:
   - versions:
@@ -32,3 +34,4 @@ output:
 
 authors:
   - "@erikrikarddaniel"
+  - "@FriederikeHanssen"

tests/modules/cat/cat/main.nf

@@ -2,53 +2,60 @@
 
 nextflow.enable.dsl = 2
 
-include { CAT_CAT } from '../../../../modules/cat/cat/main.nf'
+include { CAT_CAT                        } from '../../../../modules/cat/cat/main.nf'
+include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../modules/cat/cat/main.nf'
+include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../modules/cat/cat/main.nf'
 
 workflow test_cat_unzipped_unzipped {
 
     input = [
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) ]
     ]
 
-    CAT_CAT ( input, 'cat.txt' )
+    CAT_CAT ( input )
 }
 
 workflow test_cat_zipped_zipped {
 
     input = [
-        file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
+         [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+        [file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
     ]
 
-    CAT_CAT ( input, 'cat.txt.gz' )
+    CAT_CAT ( input )
 }
 
 workflow test_cat_zipped_unzipped {
 
     input = [
-        file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
+        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+        [file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
     ]
 
-    CAT_CAT ( input, 'cat.txt' )
+    CAT_ZIPPED_UNZIPPED ( input )
 }
 
 workflow test_cat_unzipped_zipped {
 
     input = [
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+        [file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)]
     ]
 
-    CAT_CAT ( input, 'cat.txt.gz' )
+    CAT_UNZIPPED_ZIPPED ( input )
 }
 
 workflow test_cat_one_file_unzipped_zipped {
 
     input = [
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
-    CAT_CAT ( input, 'cat.txt.gz' )
+    CAT_UNZIPPED_ZIPPED ( input )
 }

tests/modules/cat/cat/nextflow.config

@@ -2,4 +2,12 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: CAT_UNZIPPED_ZIPPED {
+        ext.prefix = 'cat.txt.gz'
+    }
+
+    withName: CAT_ZIPPED_UNZIPPED {
+        ext.prefix = 'cat.txt'
+    }
 }
+

tests/modules/cat/cat/test.yml

@@ -4,7 +4,7 @@
     - cat
     - cat/cat
   files:
-    - path: output/cat/cat.txt
+    - path: output/cat/test.fasta
       md5sum: f44b33a0e441ad58b2d3700270e2dbe2
 
 - name: cat zipped zipped
@@ -13,7 +13,7 @@
     - cat
     - cat/cat
   files:
-    - path: output/cat/cat.txt.gz
+    - path: output/cat/test.gz
 
 - name: cat zipped unzipped
   command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config