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Fixing vcftools and bismark tests (#383)

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* fixed vcftools

* fixed genomepreparation, methylationextractor

* fixed deduplicate
This commit is contained in:
Kevin Menden 2021-03-25 10:12:08 +01:00 committed by GitHub
parent 13bd67ed8a
commit 6973df628f
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GPG key ID: 4AEE18F83AFDEB23
7 changed files with 19 additions and 19 deletions
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10
tests/software/bismark/align/main.nf
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@ -11,9 +11,9 @@ include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark
*/ */
workflow test_bismark_align_single_end { workflow test_bismark_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta ) BISMARK_GENOMEPREPARATION ( fasta )
BISMARK_ALIGN_SE ( input, BISMARK_GENOMEPREPARATION.out.index ) BISMARK_ALIGN_SE ( input, BISMARK_GENOMEPREPARATION.out.index )
@ -24,10 +24,10 @@ workflow test_bismark_align_single_end {
*/ */
workflow test_bismark_align_paired_end { workflow test_bismark_align_paired_end {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta ) BISMARK_GENOMEPREPARATION ( fasta )
BISMARK_ALIGN_PE ( input, BISMARK_GENOMEPREPARATION.out.index ) BISMARK_ALIGN_PE ( input, BISMARK_GENOMEPREPARATION.out.index )

2
tests/software/bismark/deduplicate/main.nf
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@ -6,7 +6,7 @@ include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/m
workflow test_bismark_deduplicate { workflow test_bismark_deduplicate {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ]
] ]
BISMARK_DEDUPLICATE ( input ) BISMARK_DEDUPLICATE ( input )

2
tests/software/bismark/genomepreparation/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] ) include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
workflow test_bismark_genomepreparation { workflow test_bismark_genomepreparation {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta ) BISMARK_GENOMEPREPARATION ( fasta )
} }

2
tests/software/bismark/genomepreparation/test.yml
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@ -4,7 +4,7 @@
- bismark - bismark
- bismark_genomepreparation - bismark_genomepreparation
files: files:
- path: ./output/bismark/BismarkIndex/test_genome.fasta - path: ./output/bismark/BismarkIndex/genome.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6 md5sum: 6e9fe4042a72f2345f644f239272b7e6
- path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
md5sum: 903b9f357eea4a5f36e21e78e0fe1dfa md5sum: 903b9f357eea4a5f36e21e78e0fe1dfa

4
tests/software/bismark/methylationextractor/main.nf
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@ -7,9 +7,9 @@ include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/meth
workflow test_bismark_methylationextractor { workflow test_bismark_methylationextractor {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_bam'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta ) BISMARK_GENOMEPREPARATION ( fasta )
BISMARK_METHYLATIONEXTRACTOR ( input, BISMARK_GENOMEPREPARATION.out.index ) BISMARK_METHYLATIONEXTRACTOR ( input, BISMARK_GENOMEPREPARATION.out.index )

6
tests/software/bismark/report/main.nf
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@ -10,10 +10,10 @@ include { BISMARK_REPORT } from '../../../../software/bismark/repo
workflow test_bismark_report { workflow test_bismark_report {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta ) BISMARK_GENOMEPREPARATION ( fasta )
BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index ) BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )

12
tests/software/vcftools/main.nf
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@ -7,7 +7,7 @@ include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../software/vcftools/main.
workflow test_vcftools_vcf_base { workflow test_vcftools_vcf_base {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
] ]
VCFTOOLS_BASE ( input, [], [] ) VCFTOOLS_BASE ( input, [], [] )
@ -15,7 +15,7 @@ workflow test_vcftools_vcf_base {
workflow test_vcftools_vcfgz_base { workflow test_vcftools_vcfgz_base {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
] ]
VCFTOOLS_BASE ( input, [], [] ) VCFTOOLS_BASE ( input, [], [] )
@ -23,18 +23,18 @@ workflow test_vcftools_vcfgz_base {
workflow test_vcftools_vcf_optional { workflow test_vcftools_vcf_optional {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
] ]
bed = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
VCFTOOLS_OPTIONAL ( input, bed, [] ) VCFTOOLS_OPTIONAL ( input, bed, [] )
} }
workflow test_vcftools_vcfgz_optional { workflow test_vcftools_vcfgz_optional {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
] ]
bed = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
VCFTOOLS_OPTIONAL ( input, bed, [] ) VCFTOOLS_OPTIONAL ( input, bed, [] )
} }