-
Notifications
You must be signed in to change notification settings - Fork 695
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* add specific files created * typo * add from nf-test template * remove from pytest_modules * update environement file * update arriba * add tests * use latest conda build * arriba conda env * update environement * update meta * update tags in test * move arriba test to stubs as timeout for merge queue
- Loading branch information
Showing
14 changed files
with
281 additions
and
242 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,5 +1,8 @@ | ||
--- | ||
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
|
||
dependencies: | ||
- bioconda::arriba=2.4.0 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,107 @@ | ||
|
||
nextflow_process { | ||
|
||
name "Test Process ARRIBA_ARRIBA" | ||
script "../main.nf" | ||
process "ARRIBA_ARRIBA" | ||
|
||
tag "modules" | ||
tag "modules_nfcore" | ||
tag "arriba" | ||
tag "arriba/arriba" | ||
tag "arriba/download" | ||
tag "star/genomegenerate" | ||
tag "star/align" | ||
|
||
setup { | ||
config "./nextflow.config" | ||
options "-stub" | ||
run("ARRIBA_DOWNLOAD") { | ||
script "../../../arriba/download/main.nf" | ||
process { | ||
""" | ||
input[0] = 'GRCh38' | ||
""" | ||
} | ||
} | ||
run("STAR_GENOMEGENERATE") { | ||
script "../../../star/genomegenerate/main.nf" | ||
options "-stub" | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test_fasta' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] | ||
]) | ||
input[1] = Channel.of([ | ||
[ id:'test_gtf' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
]) | ||
""" | ||
} | ||
} | ||
run("STAR_ALIGN") { | ||
script "../../../star/align/main.nf" | ||
options "-stub" | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test', single_end:false ], // meta map | ||
[ | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) | ||
] | ||
]) | ||
input[1] = STAR_GENOMEGENERATE.out.index | ||
input[2] = Channel.of([ | ||
[ id:'test_gtf' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
]) | ||
input[3] = false | ||
input[4] = 'illumina' | ||
input[5] = false | ||
""" | ||
} | ||
} | ||
} | ||
|
||
test("homo_sapiens - paired_end - stub") { | ||
|
||
options "-stub" | ||
|
||
when { | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test', single_end:false ], // meta map | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true) ] | ||
]) | ||
input[1] = Channel.of([ | ||
[ id:'test_fasta' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] | ||
]) | ||
input[2] = Channel.of([ | ||
[ id:'test_gtf' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
]) | ||
input[3] = [] | ||
input[4] = [] | ||
input[5] = [] | ||
input[6] = [] | ||
""" | ||
} | ||
} | ||
|
||
then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
|
||
} | ||
|
||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,55 @@ | ||
{ | ||
"homo_sapiens - paired_end - stub": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"1": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"2": [ | ||
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" | ||
], | ||
"fusions": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"fusions_fail": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"versions": [ | ||
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.0", | ||
"nextflow": "24.04.4" | ||
}, | ||
"timestamp": "2024-10-08T15:41:23.945072" | ||
} | ||
} |
5 changes: 0 additions & 5 deletions
5
...les/nf-core/arriba/arriba/nextflow.config → ...-core/arriba/arriba/tests/nextflow.config
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,13 +1,8 @@ | ||
process { | ||
|
||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
|
||
withName: STAR_GENOMEGENERATE { | ||
ext.args = '--genomeSAindexNbases 11' | ||
} | ||
|
||
withName: STAR_ALIGN { | ||
ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' | ||
} | ||
|
||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.