modified the samtools/fastq module (#339)

* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

Co-authored-by: suzannejin <suzanne.jin@crg.eu>

software/samtools/fastq/main.nf

@@ -22,19 +22,20 @@ process SAMTOOLS_FASTQ {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.fastq"), emit: fastq
+    tuple val(meta), path("*.fastq.gz"), emit: fastq
     path  "*.version.txt"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz"
+
     """
-    samtools \\
-        fastq \\
+    samtools fastq \\
         $options.args \\
         -@ $task.cpus \\
-        $bam \\
-        > ${bam}.fastq
-
+        $endedness \\
+        $bam
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
     """
 }

software/samtools/fastq/meta.yml

@@ -1,10 +1,9 @@
 name: samtools_fastq
-description: Converts a SAM/BAM/CRAM file to FASTA or FASTQ
+description: Converts a SAM/BAM/CRAM file to FASTQ
 keywords:
     - bam
     - sam
     - cram
-    - fasta
     - fastq
 tools:
     - samtools:
@@ -33,8 +32,8 @@ output:
             e.g. [ id:'test', single_end:false ]
     - fasta:
         type: file
-        description: FASTA/FASTQ file
-        pattern: "*.{fasta,fastq}"
+        description: compressed FASTQ file
+        pattern: "*.fastq.gz"
     - version:
         type: file
         description: File containing software version

tests/software/samtools/fastq/test.yml

@@ -1,8 +1,10 @@
 - name: samtools fastq test_samtools_fastq
   command: nextflow run tests/software/samtools/fastq -entry test_samtools_fastq -c tests/config/nextflow.config
   tags:
-    - samtools_fastq
     - samtools
+    - samtools_fastq
   files:
-    - path: output/samtools/test_paired_end.sorted.bam.fastq
-      md5sum: 4863ac55a2781962dba179a929673535
+    - path: output/samtools/test_2.fastq.gz
+      md5sum: 42d3afede8c7ef21577fcd3d07edaa83
+    - path: output/samtools/test_1.fastq.gz
+      md5sum: 166feed91e5109214b0a7a0d8c53641d