Refactor cat/cat module (#723)

* Refactor cat/cat module

* Change gzip terminology

modules/cat/cat/main.nf

@@ -18,22 +18,36 @@ process CAT_CAT {
     }
 
     input:
-    path files
+    path files_in
+    val  file_out
 
     output:
-    path "file*"        , emit: file
+    path "${file_out}*" , emit: file_out
     path "*.version.txt", emit: version
 
     script:
-    def software = getSoftwareName(task.process)
-    cpus = Math.floor(task.cpus/2).toInteger()
+    def file_list = files_in.collect { it.toString() }
+    if (file_list.size > 1) {
 
-    // Use options.suffix if specified, otherwise .out; add .gz if first input file has it
-    suffix  = options.suffix ? "${options.suffix}" : ".out"
-    suffix += files[0].name =~ /\.gz/ ? '.gz' : ''
+        // | input     | output     | command1 | command2 |
+        // |-----------|------------|----------|----------|
+        // | gzipped   | gzipped    | cat      |          |
+        // | ungzipped | ungzipped  | cat      |          |
+        // | gzipped   | ungzipped  | zcat     |          |
+        // | ungzipped | gzipped    | cat      | pigz     |
 
-    """
-    cat ${options.args} $files ${options.args2} > file${suffix}
-    cat --version | grep 'GNU coreutils' | sed 's/cat (GNU coreutils) //' > ${software}.version.txt
-    """
+        def in_zip   = file_list[0].endsWith('.gz')
+        def out_zip  = file_out.endsWith('.gz')
+        def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
+        def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $options.args2" : ''
+        """
+        $command1 \\
+            $options.args \\
+            ${file_list.join(' ')} \\
+            $command2 \\
+            > $file_out
+
+        echo \$(pigz --version 2>&1) | sed 's/pigz //g' > pigz.version.txt
+        """
+    }
 }

modules/cat/cat/meta.yml

@@ -1,33 +1,34 @@
 name: cat_cat
-description: A module for concatenation of gzipped or uncompressed files, optionally filtering the output
+description: A module for concatenation of gzipped or uncompressed files
 keywords:
   - concatenate
   - gzip
-  - filter
+  - cat
 tools:
   - cat:
       description: Just concatenation
       homepage: None
-      documentation: None
+      documentation: https://man7.org/linux/man-pages/man1/cat.1.html
       tool_dev_url: None
-      doi: ""
-      licence: ""
 
 input:
-  - files:
+  - files_in:
       type: file
-      description: Gzipped or not files
+      description: List of compressed / uncompressed files
       pattern: "*"
+  - file_out:
+      type: value
+      description: Full name of output file with or without .gz extension
 
 output:
   - version:
       type: file
       description: File containing version of the pigz software
       pattern: "*.{version.txt}"
-  - bam:
+  - file_out:
       type: file
-      description: Concatenated, optionally filtered, file, gzipped if input was, otherwise not
-      pattern: "file*"
+      description: Concatenated file. Will be gzipped if file_out ends with ".gz"
+      pattern: "${file_out}"
 
 authors:
   - "@erikrikarddaniel"

tests/modules/cat/cat/main.nf

@@ -3,44 +3,43 @@
 nextflow.enable.dsl = 2
 
 include { CAT_CAT } from '../../../../modules/cat/cat/main.nf' addParams( options: [:] )
-include { CAT_CAT as CAT_CAT_SUFFIX } from '../../../../modules/cat/cat/main.nf' addParams( options: [suffix: ".fna"] )
 
-workflow test_cat_ungzipped {
-    
+workflow test_cat_unzipped_unzipped {
+
     input = [
         file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
         file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
     ]
 
-    CAT_CAT ( input )
+    CAT_CAT ( input, 'cat.txt' )
 }
 
-workflow test_cat_gzipped {
-    
+workflow test_cat_zipped_zipped {
+
     input = [
         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_CAT ( input, 'cat.txt.gz' )
 }
 
-workflow test_cat_ungzipped_fna {
-    
+workflow test_cat_zipped_unzipped {
+
+    input = [
+        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' )
+}
+
+workflow test_cat_unzipped_zipped {
+
     input = [
         file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
         file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
     ]
 
-    CAT_CAT_SUFFIX ( input )
-}
-
-workflow test_cat_gzipped_fna {
-    
-    input = [
-        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_SUFFIX ( input )
+    CAT_CAT ( input, 'cat.txt.gz' )
 }

tests/modules/cat/cat/test.yml

@@ -1,33 +1,33 @@
-- name: cat ungzipped
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_ungzipped -c tests/config/nextflow.config
+- name: cat unzipped unzipped
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c tests/config/nextflow.config
   tags:
     - cat
     - cat/cat
   files:
-    - path: output/cat/file.out
+    - path: output/cat/cat.txt
       md5sum: f44b33a0e441ad58b2d3700270e2dbe2
 
-- name: cat gzipped
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_gzipped -c tests/config/nextflow.config
+- name: cat zipped zipped
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c tests/config/nextflow.config
   tags:
     - cat
     - cat/cat
   files:
-    - path: output/cat/file.out.gz
+    - path: output/cat/cat.txt.gz
 
-- name: cat ungzipped suffix
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_ungzipped_fna -c tests/config/nextflow.config
+- name: cat zipped unzipped
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c tests/config/nextflow.config
   tags:
     - cat
     - cat/cat
   files:
-    - path: output/cat/file.fna
-      md5sum: f44b33a0e441ad58b2d3700270e2dbe2
+    - path: output/cat/cat.txt
+      md5sum: c439d3b60e7bc03e8802a451a0d9a5d9
 
-- name: cat gzipped suffix
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_gzipped_fna -c tests/config/nextflow.config
+- name: cat unzipped zipped
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c tests/config/nextflow.config
   tags:
     - cat
     - cat/cat
   files:
-    - path: output/cat/file.fna.gz
+    - path: output/cat/cat.txt.gz