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Update test paths in bwa mappers (#387)

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* Update test paths in bwa mappers

* Fix indentation

* indices pass lcoally now

* no idea how they could ever pass before, Tests pass locally no

* Update samtools and bwamem2 versions

* Correct mulled containers + md5
This commit is contained in:
FriederikeHanssen 2021-03-25 10:24:21 +01:00 committed by GitHub
parent 6973df628f
commit 555f1710e0
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GPG key ID: 4AEE18F83AFDEB23
11 changed files with 55 additions and 55 deletions
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6
software/bwa/mem/main.nf
View file

@ -11,11 +11,11 @@ process BWA_MEM {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null) conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
} else { } else {
container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
} }
input: input:

6
software/bwamem2/index/main.nf
View file

@ -11,11 +11,11 @@ process BWAMEM2_INDEX {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? "bioconda::bwa-mem2=2.1" : null) conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwa-mem2:2.1--he513fc3_0" container "https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0"
} else { } else {
container "quay.io/biocontainers/bwa-mem2:2.1--he513fc3_0" container "quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0"
} }
input: input:

6
software/bwamem2/mem/main.nf
View file

@ -11,11 +11,11 @@ process BWAMEM2_MEM {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bwa-mem2=2.1 bioconda::samtools=1.11" : null) conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0" container "https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
} else { } else {
container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0" container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
} }
input: input:

2
tests/software/bwa/index/main.nf
View file

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

10
tests/software/bwa/index/test.yml
View file

@ -4,13 +4,13 @@
- bwa - bwa
- bwa_index - bwa_index
files: files:
- path: ./output/index/bwa/test_genome.bwt - path: ./output/index/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: ./output/index/bwa/test_genome.amb - path: ./output/index/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/index/bwa/test_genome.sa - path: ./output/index/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1 md5sum: ab3952cabf026b48cd3eb5bccbb636d1
- path: ./output/index/bwa/test_genome.pac - path: ./output/index/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/index/bwa/test_genome.ann - path: ./output/index/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567

10
tests/software/bwa/mem/main.nf
View file

@ -10,9 +10,9 @@ include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( optio
*/ */
workflow test_bwa_mem_single_end { workflow test_bwa_mem_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta ) BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index ) BWA_MEM ( input, BWA_INDEX.out.index )
@ -23,10 +23,10 @@ workflow test_bwa_mem_single_end {
*/ */
workflow test_bwa_mem_paired_end { workflow test_bwa_mem_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) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta ) BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index ) BWA_MEM ( input, BWA_INDEX.out.index )

24
tests/software/bwa/mem/test.yml
View file

@ -6,16 +6,16 @@
- bwa_mem_single_end - bwa_mem_single_end
files: files:
- path: ./output/bwa/test.bam - path: ./output/bwa/test.bam
md5sum: c0d98ef222409eca3b7347bfd91484ba md5sum: 9165508bf914baee0e6347711aa7b23a
- path: ./output/bwa/bwa/test_genome.bwt - path: ./output/index/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: ./output/bwa/bwa/test_genome.amb - path: ./output/index/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/bwa/bwa/test_genome.ann - path: ./output/index/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567
- path: ./output/bwa/bwa/test_genome.pac - path: ./output/index/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwa/bwa/test_genome.sa - path: ./output/index/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1 md5sum: ab3952cabf026b48cd3eb5bccbb636d1
- name: bwa mem paired-end - name: bwa mem paired-end
@ -26,14 +26,14 @@
- bwa_mem_paired_end - bwa_mem_paired_end
files: files:
- path: ./output/bwa/test.bam - path: ./output/bwa/test.bam
md5sum: dcb1c0d42496b582ddb4e8e892b47c4e md5sum: 670a53bddee62d6bd14ed7adaf103e7c
- path: ./output/bwa/bwa/test_genome.bwt - path: ./output/index/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: ./output/bwa/bwa/test_genome.amb - path: ./output/index/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/bwa/bwa/test_genome.ann - path: ./output/index/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567
- path: ./output/bwa/bwa/test_genome.pac - path: ./output/index/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwa/bwa/test_genome.sa - path: ./output/index/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1 md5sum: ab3952cabf026b48cd3eb5bccbb636d1

2
tests/software/bwamem2/index/main.nf
View file

@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] ) include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] )
workflow test_bwamem2_index { workflow test_bwamem2_index {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMEM2_INDEX ( fasta ) BWAMEM2_INDEX ( fasta )
} }

10
tests/software/bwamem2/index/test.yml
View file

@ -4,13 +4,13 @@
- bwamem2 - bwamem2
- bwamem2_index - bwamem2_index
files: files:
- path: ./output/index/bwamem2/test_genome.fasta.amb - path: ./output/index/bwamem2/genome.fasta.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/index/bwamem2/test_genome.fasta.pac - path: ./output/index/bwamem2/genome.fasta.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/index/bwamem2/test_genome.fasta.0123 - path: ./output/index/bwamem2/genome.fasta.0123
md5sum: b02870de80106104abcb03cd9463e7d8 md5sum: b02870de80106104abcb03cd9463e7d8
- path: ./output/index/bwamem2/test_genome.fasta.bwt.2bit.64 - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
md5sum: d097a1b82dee375d41a1ea69895a9216 md5sum: d097a1b82dee375d41a1ea69895a9216
- path: ./output/index/bwamem2/test_genome.fasta.ann - path: ./output/index/bwamem2/genome.fasta.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567

10
tests/software/bwamem2/mem/main.nf
View file

@ -10,9 +10,9 @@ include { BWAMEM2_MEM } from '../../../../software/bwamem2/mem/main.nf' addP
*/ */
workflow test_bwamem2_mem_single_end { workflow test_bwamem2_mem_single_end {
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMEM2_INDEX ( fasta ) BWAMEM2_INDEX ( fasta )
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index ) BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
@ -23,10 +23,10 @@ workflow test_bwamem2_mem_single_end {
*/ */
workflow test_bwamem2_mem_paired_end { workflow test_bwamem2_mem_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) ]
] ]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMEM2_INDEX ( fasta ) BWAMEM2_INDEX ( fasta )
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index ) BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )

24
tests/software/bwamem2/mem/test.yml
View file

@ -6,16 +6,16 @@
- bwamem2_mem_single_end - bwamem2_mem_single_end
files: files:
- path: ./output/bwamem2/test.bam - path: ./output/bwamem2/test.bam
md5sum: b0823bb56a248a6870be51d26851214e md5sum: 2133c011119ea11f06f0a9b1621ba05b
- path: ./output/bwamem2/bwamem2/test_genome.fasta.amb - path: ./output/index/bwamem2/genome.fasta.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/bwamem2/bwamem2/test_genome.fasta.pac - path: ./output/index/bwamem2/genome.fasta.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwamem2/bwamem2/test_genome.fasta.0123 - path: ./output/index/bwamem2/genome.fasta.0123
md5sum: b02870de80106104abcb03cd9463e7d8 md5sum: b02870de80106104abcb03cd9463e7d8
- path: ./output/bwamem2/bwamem2/test_genome.fasta.bwt.2bit.64 - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
md5sum: d097a1b82dee375d41a1ea69895a9216 md5sum: d097a1b82dee375d41a1ea69895a9216
- path: ./output/bwamem2/bwamem2/test_genome.fasta.ann - path: ./output/index/bwamem2/genome.fasta.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567
- name: bwamem2 mem paired-end - name: bwamem2 mem paired-end
@ -26,14 +26,14 @@
- bwamem2_mem_paired_end - bwamem2_mem_paired_end
files: files:
- path: ./output/bwamem2/test.bam - path: ./output/bwamem2/test.bam
md5sum: bd938bf4038759be9c872394927eec05 md5sum: d8fadab5cef04faff1851a8162fc30b5
- path: ./output/bwamem2/bwamem2/test_genome.fasta.amb - path: ./output/index/bwamem2/genome.fasta.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/bwamem2/bwamem2/test_genome.fasta.pac - path: ./output/index/bwamem2/genome.fasta.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwamem2/bwamem2/test_genome.fasta.0123 - path: ./output/index/bwamem2/genome.fasta.0123
md5sum: b02870de80106104abcb03cd9463e7d8 md5sum: b02870de80106104abcb03cd9463e7d8
- path: ./output/bwamem2/bwamem2/test_genome.fasta.bwt.2bit.64 - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
md5sum: d097a1b82dee375d41a1ea69895a9216 md5sum: d097a1b82dee375d41a1ea69895a9216
- path: ./output/bwamem2/bwamem2/test_genome.fasta.ann - path: ./output/index/bwamem2/genome.fasta.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567