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Code Issues Releases Packages Activity

Fixing a bunch of module tests (#370)

Browse source 
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

* fixing a bunch of module tests

* remove vscode

* fixed minia

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Kevin Menden 2021-03-24 18:36:29 +01:00 committed by GitHub
parent 0337916f8a
commit 04c3684db7
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GPG key ID: 4AEE18F83AFDEB23
6 changed files with 11 additions and 12 deletions
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2
tests/software/gffread/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { GFFREAD } from '../../../software/gffread/main.nf' addParams( options: [:] )
workflow test_gffread {
input = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gff3", checkIfExists: true)
input = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
GFFREAD ( input )
}

4
tests/software/gffread/test.yml
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@ -3,5 +3,5 @@
tags:
- gffread
files:
- path: ./output/gffread/test_genome.gtf
md5sum: 330c31462457cf1817827518126ff7c5
- path: ./output/gffread/genome.gtf
md5sum: f184f856b7fe3e159d21b052b5dd3954

7
tests/software/homer/annotatepeaks/main.nf
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@ -6,10 +6,9 @@ include { HOMER_ANNOTATEPEAKS } from '../../../../software/homer/annotatepeaks/m
workflow test_homer_annotatepeaks {
input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
HOMER_ANNOTATEPEAKS ( input, fasta, gtf )
}

4
tests/software/minia/main.nf
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@ -6,8 +6,8 @@ include { MINIA } from '../../../software/minia/main.nf' addParams( options: [:]
workflow test_minia {
input = [ [ id:'test' ], // meta map
[file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)]
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
]
MINIA ( input )

2
tests/software/sequenzautils/gcwiggle/main.nf
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@ -6,7 +6,7 @@ include { SEQUENZAUTILS_GCWIGGLE } from '../../../../software/sequenzautils/gcwi
workflow test_sequenzautils_gcwiggle {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
SEQUENZAUTILS_GCWIGGLE ( input )

4
tests/software/seqwish/induce/main.nf
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@ -6,8 +6,8 @@ include { SEQWISH_INDUCE } from '../../../../software/seqwish/induce/main.nf' ad
workflow test_seqwish_induce {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.paf", checkIfExists: true) ],
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['genome']['transcriptome_paf'], checkIfExists: true)],
[ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
]
SEQWISH_INDUCE ( input )