From c5a5e25129eff29d5216146f699a551cdbdbb3e8 Mon Sep 17 00:00:00 2001 From: Anthony Fullam Date: Wed, 24 Mar 2021 19:18:01 +0100 Subject: [PATCH] Update test data paths. (#375) * Updata test data paths. * Remove quote * Revert quast * Fix broken test * Update md5 --- tests/software/allelecounter/main.nf | 6 +++--- tests/software/cnvkit/main.nf | 8 ++++---- tests/software/cutadapt/main.nf | 6 +++--- tests/software/gunzip/main.nf | 2 +- tests/software/ivar/consensus/main.nf | 4 ++-- tests/software/ivar/trim/main.nf | 6 +++--- tests/software/ivar/trim/test.yml | 2 +- tests/software/ivar/variants/main.nf | 14 +++++++------- tests/software/prodigal/main.nf | 2 +- tests/software/prokka/main.nf | 2 +- 10 files changed, 26 insertions(+), 26 deletions(-) diff --git a/tests/software/allelecounter/main.nf b/tests/software/allelecounter/main.nf index 11a04611..08f6129c 100644 --- a/tests/software/allelecounter/main.nf +++ b/tests/software/allelecounter/main.nf @@ -5,10 +5,10 @@ include { ALLELECOUNTER } from '../../../software/allelecounter/main.nf' addPara workflow test_allelecounter { input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), - file("${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'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - positions = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ] + positions = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] ALLELECOUNTER ( input, positions ) } diff --git a/tests/software/cnvkit/main.nf b/tests/software/cnvkit/main.nf index 643150a2..6f922af1 100755 --- a/tests/software/cnvkit/main.nf +++ b/tests/software/cnvkit/main.nf @@ -5,15 +5,15 @@ nextflow.enable.dsl = 2 include { CNVKIT } from '../../../software/cnvkit/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] ) workflow test_cnvkit { - tumourbam = file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) - normalbam = file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam", checkIfExists: true) + tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) input = [ [ id:'test' ], // meta map tumourbam, normalbam ] - fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) - targets = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true) CNVKIT ( input, fasta, targets ) } diff --git a/tests/software/cutadapt/main.nf b/tests/software/cutadapt/main.nf index 8c1d6d26..4e44300d 100644 --- a/tests/software/cutadapt/main.nf +++ b/tests/software/cutadapt/main.nf @@ -9,7 +9,7 @@ include { CUTADAPT } from '../../../software/cutadapt/main.nf' addParams( optio */ workflow test_cutadapt_single_end { input = [ [ id:'test', single_end:true ], // meta map - [ file("${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 ) @@ -21,8 +21,8 @@ workflow test_cutadapt_single_end { workflow test_cutadapt_paired_end { input = [ [ id:'test', single_end:false ], // 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) ] ] CUTADAPT ( input ) diff --git a/tests/software/gunzip/main.nf b/tests/software/gunzip/main.nf index 8944a874..4d458a5f 100644 --- a/tests/software/gunzip/main.nf +++ b/tests/software/gunzip/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { GUNZIP } from '../../../software/gunzip/main.nf' addParams( options: [:] ) workflow test_gunzip { - input = file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) + input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) GUNZIP ( input ) } diff --git a/tests/software/ivar/consensus/main.nf b/tests/software/ivar/consensus/main.nf index e74edd6c..29dd564b 100644 --- a/tests/software/ivar/consensus/main.nf +++ b/tests/software/ivar/consensus/main.nf @@ -7,9 +7,9 @@ include { IVAR_CONSENSUS } from '../../../../software/ivar/consensus/main.nf' ad workflow test_ivar_consensus { input = [ [ id:'test'], - file("${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("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) IVAR_CONSENSUS ( input, fasta ) } diff --git a/tests/software/ivar/trim/main.nf b/tests/software/ivar/trim/main.nf index 034540dc..ab87ee9a 100644 --- a/tests/software/ivar/trim/main.nf +++ b/tests/software/ivar/trim/main.nf @@ -6,10 +6,10 @@ include { IVAR_TRIM } from '../../../../software/ivar/trim/main.nf' addParams([: workflow test_ivar_trim { input = [ [ id:'test'], - file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - bed = file("${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 ) } diff --git a/tests/software/ivar/trim/test.yml b/tests/software/ivar/trim/test.yml index b8fac63b..6879ce6f 100644 --- a/tests/software/ivar/trim/test.yml +++ b/tests/software/ivar/trim/test.yml @@ -5,4 +5,4 @@ - ivar_trim files: - path: output/ivar/test.bam - md5sum: d5cf5bda0c47c40d70193fbe6c4c828f + md5sum: 8705d032b28a1c3dbfe78fa762a2132f diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf index 2a151867..bafb3d18 100644 --- a/tests/software/ivar/variants/main.nf +++ b/tests/software/ivar/variants/main.nf @@ -9,9 +9,9 @@ workflow test_ivar_variants_no_gff_no_mpileup { params.save_mpileup = false 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") IVAR_VARIANTS ( input, fasta, dummy ) @@ -22,9 +22,9 @@ workflow test_ivar_variants_no_gff_with_mpileup { params.save_mpileup = true 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") IVAR_VARIANTS ( input, fasta, dummy ) @@ -35,10 +35,10 @@ workflow test_ivar_variants_with_gff_with_mpileup { params.save_mpileup = true 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) - gff = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) IVAR_VARIANTS ( input, fasta, gff ) } diff --git a/tests/software/prodigal/main.nf b/tests/software/prodigal/main.nf index 564a85bd..fe099425 100644 --- a/tests/software/prodigal/main.nf +++ b/tests/software/prodigal/main.nf @@ -6,7 +6,7 @@ include { PRODIGAL } from '../../../software/prodigal/main.nf' addParams( option workflow test_prodigal { input = [ [ id:'test' ], // meta map - file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] PRODIGAL ( input , "gff") diff --git a/tests/software/prokka/main.nf b/tests/software/prokka/main.nf index 15ff5665..e230f064 100644 --- a/tests/software/prokka/main.nf +++ b/tests/software/prokka/main.nf @@ -6,7 +6,7 @@ include { PROKKA } from '../../../software/prokka/main.nf' addParams( options: [ workflow test_prokka { 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, [], [] )