Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)

* Rename process from STRINGTIE to STRINGTIE_STRINGTIE

* Bump Stringtie version to 2.2.1 and remove empty files in tests

* Fix tests for stringtie/merge

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

modules/stringtie/merge/main.nf

@@ -2,10 +2,10 @@ process STRINGTIE_MERGE {
     label 'process_medium'
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda     (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
+    conda     (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
 
     input:
     path stringtie_gtf

modules/stringtie/stringtie/main.nf

@@ -1,11 +1,11 @@
-process STRINGTIE {
+process STRINGTIE_STRINGTIE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
+    conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
 
     input:
     tuple val(meta), path(bam)

modules/stringtie/stringtie/meta.yml

@@ -1,4 +1,4 @@
-name: stringtie
+name: stringtie_stringtie
 description: Transcript assembly and quantification for RNA-Se
 keywords:
   - transcript

tests/modules/stringtie/merge/main.nf

@@ -2,8 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { STRINGTIE       } from '../../../../modules/stringtie/stringtie/main.nf'
-include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
+include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_MERGE     } from '../../../../modules/stringtie/merge/main.nf'
 
 /*
  * Test with forward strandedness
@@ -15,8 +15,8 @@ workflow test_stringtie_forward_merge {
     ]
     annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
         .out
         .transcript_gtf
         .map { it -> it[1] }
@@ -35,8 +35,8 @@ workflow test_stringtie_reverse_merge {
     ]
     annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
         .out
         .transcript_gtf
         .map { it -> it[1] }

tests/modules/stringtie/merge/test.yml

@@ -5,7 +5,7 @@
     - stringtie/merge
   files:
     - path: output/stringtie/stringtie.merged.gtf
-      md5sum: 9fab7049ef2eafdea246fc787d1def40
+      md5sum: d959eb2fab0db48ded7275e0a2e83c05
     - path: output/stringtie/test.ballgown/e2t.ctab
       md5sum: 9ae42e056c955a88a883e5e917840d77
     - path: output/stringtie/test.ballgown/e_data.ctab
@@ -17,11 +17,10 @@
     - path: output/stringtie/test.ballgown/t_data.ctab
       md5sum: 92a98902784e7406ffe054d2adbabc7c
     - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 9708811bcefe0f6384293d6f419f3250
+      md5sum: 8bcd8e2730ed3337e2730186dbc184f3
     - path: output/stringtie/test.transcripts.gtf
-      md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f
+      md5sum: a914bd55b68a4b5f607738b17861e362
 
 - name: stringtie merge test_stringtie_reverse_merge
   command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
@@ -30,7 +29,7 @@
     - stringtie/merge
   files:
     - path: output/stringtie/stringtie.merged.gtf
-      md5sum: afc461bb3cbc368f268a7a45c1b54497
+      md5sum: 6da479298d73d5b3216d4e1576a2bdf4
     - path: output/stringtie/test.ballgown/e2t.ctab
       md5sum: 9ae42e056c955a88a883e5e917840d77
     - path: output/stringtie/test.ballgown/e_data.ctab
@@ -42,8 +41,7 @@
     - path: output/stringtie/test.ballgown/t_data.ctab
       md5sum: 92a98902784e7406ffe054d2adbabc7c
     - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 94b85145d60ab1b80a7f0f6cf08418b0
+      md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
     - path: output/stringtie/test.transcripts.gtf
-      md5sum: 3196e3d50fd461aae6408e0a70acae68
+      md5sum: 9dcdc9577c0fdbb25089eda210267546

tests/modules/stringtie/stringtie/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
 //
 // Test with forward strandedness
 //
@@ -13,7 +13,7 @@ workflow test_stringtie_forward {
     ]
     annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
 }
 
 //
@@ -26,5 +26,5 @@ workflow test_stringtie_reverse {
     ]
     annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
 }

tests/modules/stringtie/stringtie/test.yml

@@ -8,7 +8,6 @@
     - path: ./output/stringtie/test.gene.abundance.txt
       md5sum: 7d8bce7f2a922e367cedccae7267c22e
     - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/stringtie/test.ballgown/e_data.ctab
       md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
     - path: ./output/stringtie/test.ballgown/i_data.ctab
@@ -30,7 +29,6 @@
     - path: ./output/stringtie/test.gene.abundance.txt
       md5sum: 7385b870b955dae2c2ab78a70cf05cce
     - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/stringtie/test.ballgown/e_data.ctab
       md5sum: 879b6696029d19c4737b562e9d149218
     - path: ./output/stringtie/test.ballgown/i_data.ctab