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Fix a bunch of failing tests after switching to test config (#378)

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* Update test for trimgalore

* Fix picard markduplicate test

* Fix tests for picard mergesamfiles

* Fix checksum for markduplicates

* Fix multiplemetrics and wgsmetrics

* Fix checksum for mergesamfiles
This commit is contained in:
Gregor Sturm 2021-03-24 19:28:54 +01:00 committed by GitHub
parent 17fbdf96cb
commit 2dba72dd14
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7 changed files with 14 additions and 14 deletions
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4
tests/software/picard/collectmultiplemetrics/main.nf
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@ -6,9 +6,9 @@ include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../software/picard/coll
workflow test_picard_collectmultiplemetrics { workflow test_picard_collectmultiplemetrics {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
PICARD_COLLECTMULTIPLEMETRICS ( input, fasta ) PICARD_COLLECTMULTIPLEMETRICS ( input, fasta )
} }

6
tests/software/picard/collectwgsmetrics/main.nf
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@ -6,10 +6,10 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../software/picard/collectwg
workflow test_picard_collectwgsmetrics { workflow test_picard_collectwgsmetrics {
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)
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
PICARD_COLLECTWGSMETRICS ( input, fasta ) PICARD_COLLECTWGSMETRICS ( input, fasta )
} }

4
tests/software/picard/markduplicates/main.nf
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@ -6,7 +6,7 @@ include { PICARD_MARKDUPLICATES } from '../../../../software/picard/markduplicat
workflow test_picard_markduplicates_sorted_bam { workflow test_picard_markduplicates_sorted_bam {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
PICARD_MARKDUPLICATES ( input ) PICARD_MARKDUPLICATES ( input )
@ -14,7 +14,7 @@ workflow test_picard_markduplicates_sorted_bam {
workflow test_picard_markduplicates_unsorted_bam { workflow test_picard_markduplicates_unsorted_bam {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
PICARD_MARKDUPLICATES ( input ) PICARD_MARKDUPLICATES ( input )

2
tests/software/picard/markduplicates/test.yml
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@ -6,7 +6,7 @@
files: files:
- path: ./output/picard/test.MarkDuplicates.metrics.txt - path: ./output/picard/test.MarkDuplicates.metrics.txt
- path: ./output/picard/test.bam - path: ./output/picard/test.bam
md5sum: 19a4891c3b98d0482dce2253fb28d852 md5sum: fe8ed25b4bd25be0cc7a8730fc3b2f30
- name: picard markduplicates on unsorted bam - name: picard markduplicates on unsorted bam
command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config

4
tests/software/picard/mergesamfiles/main.nf
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@ -6,8 +6,8 @@ include { PICARD_MERGESAMFILES } from '../../../../software/picard/mergesamfiles
workflow test_picard_mergesamfiles { workflow test_picard_mergesamfiles {
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_single_end.bam", checkIfExists: true), ] file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true), ]
] ]
PICARD_MERGESAMFILES ( input ) PICARD_MERGESAMFILES ( input )

2
tests/software/picard/mergesamfiles/test.yml
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@ -5,4 +5,4 @@
- picard_mergesamfiles - picard_mergesamfiles
files: files:
- path: ./output/picard/test.bam - path: ./output/picard/test.bam
md5sum: 58c55f222b48df0a536cb635593388a4 md5sum: b8bd6c22f36c6ebc91bca98bd637a2eb

6
tests/software/trimgalore/main.nf
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@ -9,7 +9,7 @@ include { TRIMGALORE } from '../../../software/trimgalore/main.nf' addParams( op
*/ */
workflow test_trimgalore_single_end { workflow test_trimgalore_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
] ]
TRIMGALORE ( input ) TRIMGALORE ( input )
@ -20,8 +20,8 @@ workflow test_trimgalore_single_end {
*/ */
workflow test_trimgalore_paired_end { workflow test_trimgalore_paired_end {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${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) ]
] ]
TRIMGALORE ( input ) TRIMGALORE ( input )