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Update test data paths. (#375)

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* Updata test data paths.

* Remove quote

* Revert quast

* Fix broken test

* Update md5
This commit is contained in:
Anthony Fullam 2021-03-24 19:18:01 +01:00 committed by GitHub
parent d162f21ab3
commit c5a5e25129
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GPG key ID: 4AEE18F83AFDEB23
10 changed files with 26 additions and 26 deletions
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6
tests/software/allelecounter/main.nf
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@ -5,10 +5,10 @@ include { ALLELECOUNTER } from '../../../software/allelecounter/main.nf' addPara
workflow test_allelecounter { workflow test_allelecounter {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
positions = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ] positions = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
ALLELECOUNTER ( input, positions ) ALLELECOUNTER ( input, positions )
} }

8
tests/software/cnvkit/main.nf
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@ -5,15 +5,15 @@ nextflow.enable.dsl = 2
include { CNVKIT } from '../../../software/cnvkit/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] ) include { CNVKIT } from '../../../software/cnvkit/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] )
workflow test_cnvkit { workflow test_cnvkit {
tumourbam = file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
normalbam = file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam", checkIfExists: true) normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
tumourbam, tumourbam,
normalbam normalbam
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
targets = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true) targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
CNVKIT ( input, fasta, targets ) CNVKIT ( input, fasta, targets )
} }

6
tests/software/cutadapt/main.nf
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@ -9,7 +9,7 @@ include { CUTADAPT } from '../../../software/cutadapt/main.nf' addParams( optio
*/ */
workflow test_cutadapt_single_end { workflow test_cutadapt_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
] ]
CUTADAPT ( input ) CUTADAPT ( input )
@ -21,8 +21,8 @@ workflow test_cutadapt_single_end {
workflow test_cutadapt_paired_end { workflow test_cutadapt_paired_end {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['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_2_fastq_gz'], checkIfExists: true) ]
] ]
CUTADAPT ( input ) CUTADAPT ( input )

2
tests/software/gunzip/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { GUNZIP } from '../../../software/gunzip/main.nf' addParams( options: [:] ) include { GUNZIP } from '../../../software/gunzip/main.nf' addParams( options: [:] )
workflow test_gunzip { workflow test_gunzip {
input = file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
GUNZIP ( input ) GUNZIP ( input )
} }

4
tests/software/ivar/consensus/main.nf
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@ -7,9 +7,9 @@ include { IVAR_CONSENSUS } from '../../../../software/ivar/consensus/main.nf' ad
workflow test_ivar_consensus { workflow test_ivar_consensus {
input = [ [ id:'test'], input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
IVAR_CONSENSUS ( input, fasta ) IVAR_CONSENSUS ( input, fasta )
} }

6
tests/software/ivar/trim/main.nf
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@ -6,10 +6,10 @@ include { IVAR_TRIM } from '../../../../software/ivar/trim/main.nf' addParams([:
workflow test_ivar_trim { workflow test_ivar_trim {
input = [ [ id:'test'], input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
bed = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) bed_file = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
IVAR_TRIM ( input, bed_file ) IVAR_TRIM ( input, bed_file )
} }

2
tests/software/ivar/trim/test.yml
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@ -5,4 +5,4 @@
- ivar_trim - ivar_trim
files: files:
- path: output/ivar/test.bam - path: output/ivar/test.bam
md5sum: d5cf5bda0c47c40d70193fbe6c4c828f md5sum: 8705d032b28a1c3dbfe78fa762a2132f

14
tests/software/ivar/variants/main.nf
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@ -9,9 +9,9 @@ workflow test_ivar_variants_no_gff_no_mpileup {
params.save_mpileup = false params.save_mpileup = false
input = [ [ id:'test'], input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
dummy = file("dummy_file.txt") dummy = file("dummy_file.txt")
IVAR_VARIANTS ( input, fasta, dummy ) IVAR_VARIANTS ( input, fasta, dummy )
@ -22,9 +22,9 @@ workflow test_ivar_variants_no_gff_with_mpileup {
params.save_mpileup = true params.save_mpileup = true
input = [ [ id:'test'], input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
dummy = file("dummy_file.txt") dummy = file("dummy_file.txt")
IVAR_VARIANTS ( input, fasta, dummy ) IVAR_VARIANTS ( input, fasta, dummy )
@ -35,10 +35,10 @@ workflow test_ivar_variants_with_gff_with_mpileup {
params.save_mpileup = true params.save_mpileup = true
input = [ [ id:'test'], input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
gff = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gff3", checkIfExists: true) gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
IVAR_VARIANTS ( input, fasta, gff ) IVAR_VARIANTS ( input, fasta, gff )
} }

2
tests/software/prodigal/main.nf
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@ -6,7 +6,7 @@ include { PRODIGAL } from '../../../software/prodigal/main.nf' addParams( option
workflow test_prodigal { workflow test_prodigal {
input = [ [ id:'test' ], // meta map 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)
] ]
PRODIGAL ( input , "gff") PRODIGAL ( input , "gff")

2
tests/software/prokka/main.nf
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@ -6,7 +6,7 @@ include { PROKKA } from '../../../software/prokka/main.nf' addParams( options: [
workflow test_prokka { workflow test_prokka {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
] ]
PROKKA ( input, [], [] ) PROKKA ( input, [], [] )