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Rename process from STRINGTIE to STRINGTIE_STRINGTIE #1546

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merged 6 commits into from
Apr 22, 2022
Merged

Rename process from STRINGTIE to STRINGTIE_STRINGTIE #1546

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3ddbcf4
Rename process from STRINGTIE to STRINGTIE_STRINGTIE
drpatelh Apr 21, 2022
5c03d5c
Bump Stringtie version to 2.2.1 and remove empty files in tests
drpatelh Apr 21, 2022
ba1ddbc
Fix tests for stringtie/merge
drpatelh Apr 21, 2022
9cb3d2a
Merge branch 'master' into stringtie
drpatelh Apr 22, 2022
6529dbc
Merge branch 'master' into stringtie
mirpedrol Apr 22, 2022
1445201
Merge branch 'master' into stringtie
drpatelh Apr 22, 2022
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6 changes: 3 additions & 3 deletions modules/stringtie/merge/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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8 changes: 4 additions & 4 deletions modules/stringtie/stringtie/main.nf
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Original file line number Diff line number Diff line change
@@ -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)
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2 changes: 1 addition & 1 deletion modules/stringtie/stringtie/meta.yml
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@@ -1,4 +1,4 @@
name: stringtie
name: stringtie_stringtie
description: Transcript assembly and quantification for RNA-Se
keywords:
- transcript
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12 changes: 6 additions & 6 deletions tests/modules/stringtie/merge/main.nf
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Expand Up @@ -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
Expand All @@ -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] }
Expand All @@ -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] }
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14 changes: 6 additions & 8 deletions tests/modules/stringtie/merge/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
6 changes: 3 additions & 3 deletions tests/modules/stringtie/stringtie/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
//
Expand All @@ -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 )
}

//
Expand All @@ -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 )
}
2 changes: 0 additions & 2 deletions tests/modules/stringtie/stringtie/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down