Add option -p to set the # of cpus on stringtie (#601)

* Add option -p  to set  the # of cpus on stringtie

* Bump version 2.1.7 to stringtie modules

* Output stringtie/merge version

* Fix padding

* Apply suggestions from code review

* Defining software variable

* Fix test, gff can't be md5 check, contains instead

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

modules/stringtie/merge/main.nf

@@ -11,11 +11,11 @@ process STRINGTIE_MERGE {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda     (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
+    conda     (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
     } else {
-        container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
+        container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
     }
 
     input:
@@ -24,12 +24,16 @@ process STRINGTIE_MERGE {
 
     output:
     path "stringtie.merged.gtf", emit: gtf
+    path  "*.version.txt"      , emit: version
 
     script:
+    def software = getSoftwareName(task.process)
     """
     stringtie \\
         --merge $stringtie_gtf \\
         -G $annotation_gtf \\
         -o stringtie.merged.gtf
+
+    echo \$(stringtie --version 2>&1) > ${software}.version.txt
     """
 }

modules/stringtie/stringtie/main.nf

@@ -11,11 +11,11 @@ process STRINGTIE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
+    conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
     } else {
-        container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
+        container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
     }
 
     input:
@@ -48,8 +48,9 @@ process STRINGTIE {
         -A ${prefix}.gene.abundance.txt \\
         -C ${prefix}.coverage.gtf \\
         -b ${prefix}.ballgown \\
+        -p $task.cpus \\
         $options.args
 
-    stringtie --version > ${software}.version.txt
+    echo \$(stringtie --version 2>&1) > ${software}.version.txt
     """
 }

tests/modules/stringtie/merge/test.yml

@@ -5,7 +5,10 @@
     - stringtie/merge
   files:
     - path: ./output/test_stringtie_forward_merge/stringtie.merged.gtf
-      md5sum: 676aa20a2d7a3db18136cdc7ba183099
+      contains:
+      - 'stringtie'
+      - 'merge'
+      - 'chr22'
 
 - name: stringtie reverse-strand merge
   command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
@@ -14,4 +17,7 @@
     - stringtie/merge
   files:
     - path: ./output/test_stringtie_reverse_merge/stringtie.merged.gtf
-      md5sum: 67e5102722ecaeea1fb44d1ec0953474      
+      contains:
+      - 'stringtie'
+      - 'merge'
+      - 'chr22'