update: gunzip to include meta input tuple (#1082)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* fix: pigz formatting

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

* Add bamUtil trimBam

* Update modules/bamutil/trimbam/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/bamutil/trimbam/main.nf

* Changes after code-review

* YAML lint

* update: add (optional) meta to input tuple

* YAML linting

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

modules/gunzip/main.nf

@@ -9,7 +9,7 @@ process GUNZIP {
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -19,14 +19,14 @@ process GUNZIP {
     }
 
     input:
-    path archive
+    tuple val(meta), path(archive)
 
     output:
-    path "$gunzip",       emit: gunzip
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("$gunzip"), emit: gunzip
+    path "versions.yml"             , emit: versions
 
     script:
-    gunzip       = archive.toString() - '.gz'
+    gunzip = archive.toString() - '.gz'
     """
     gunzip \\
         -f \\

modules/gunzip/meta.yml

@@ -10,6 +10,11 @@ tools:
         documentation: https://www.gnu.org/software/gzip/manual/gzip.html
         licence: ['GPL-3.0-or-later']
 input:
+    - meta:
+        type: map
+        description: |
+          Optional groovy Map containing meta information
+          e.g. [ id:'test', single_end:false ]
     - archive:
         type: file
         description: File to be compressed/uncompressed
@@ -26,3 +31,4 @@ output:
 authors:
     - "@joseespinosa"
     - "@drpatelh"
+    - "@jfy133"

tests/modules/gunzip/main.nf

@@ -5,7 +5,9 @@ nextflow.enable.dsl = 2
 include { GUNZIP } from '../../../modules/gunzip/main.nf' addParams( options: [:] )
 
 workflow test_gunzip {
-    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    input = [ [],
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
 
     GUNZIP ( input )
 }