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Code Issues Releases Packages Activity

update test data paths (#373)

Browse source 
* update test data paths

* Update test md5sums

* gatk test fixes & update variantfiltration main

* few extra fixes after review

* fix suspected format error

* Update software/gatk4/variantfiltration/main.nf

* Update software/gatk4/variantfiltration/main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Mark-S-Hill 2021-03-24 18:14:11 +00:00 committed by GitHub
parent 04c3684db7
commit 889465cb2b
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GPG key ID: 4AEE18F83AFDEB23
15 changed files with 57 additions and 54 deletions
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10
software/gatk4/variantfiltration/main.nf
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@ -20,11 +20,13 @@ process GATK4_VARIANTFILTRATION {
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)
tuple path(fasta), path(fai), path(dict) path fasta
path fai
path dict
output: output:
tuple val(meta), path("*filtered.vcf"), emit: vcf tuple val(meta), path("*.vcf"), emit: vcf
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
@ -34,7 +36,7 @@ process GATK4_VARIANTFILTRATION {
gatk VariantFiltration \\ gatk VariantFiltration \\
-R $fasta \\ -R $fasta \\
-V $vcf \\ -V $vcf \\
-O ${prefix}.filtered.vcf \\ -O ${prefix}.vcf \\
$options.args $options.args
gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt

6
tests/software/bcftools/consensus/main.nf
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@ -6,9 +6,9 @@ include { BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/mai
workflow test_bcftools_consensus { workflow test_bcftools_consensus {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true) ], [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi", checkIfExists: true) ], [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) ],
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
] ]
BCFTOOLS_CONSENSUS ( input ) BCFTOOLS_CONSENSUS ( input )

6
tests/software/bcftools/consensus/test.yml
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@ -1,8 +1,8 @@
- name: bcftools consensus - name: bcftools consensus test_bcftools_consensus
command: nextflow run ./tests/software/bcftools/consensus -entry test_bcftools_consensus -c tests/config/nextflow.config command: nextflow run tests/software/bcftools/consensus -entry test_bcftools_consensus -c tests/config/nextflow.config
tags: tags:
- bcftools
- bcftools_consensus - bcftools_consensus
- bcftools
files: files:
- path: output/bcftools/test.fa - path: output/bcftools/test.fa
md5sum: e57d3e4d113f989bc069c5fd61627091 md5sum: e57d3e4d113f989bc069c5fd61627091

2
tests/software/bcftools/filter/main.nf
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@ -7,7 +7,7 @@ include { BCFTOOLS_FILTER } from '../../../../software/bcftools/filter/main.nf'
workflow test_bcftools_filter { workflow test_bcftools_filter {
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) ]
] ]
BCFTOOLS_FILTER ( input ) BCFTOOLS_FILTER ( input )

6
tests/software/bcftools/filter/test.yml
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@ -1,8 +1,8 @@
- name: bcftools filter - name: bcftools filter test_bcftools_filter
command: nextflow run ./tests/software/bcftools/filter -entry test_bcftools_filter -c tests/config/nextflow.config command: nextflow run tests/software/bcftools/filter -entry test_bcftools_filter -c tests/config/nextflow.config
tags: tags:
- bcftools
- bcftools_filter - bcftools_filter
- bcftools
files: files:
- path: output/bcftools/test.vcf.gz - path: output/bcftools/test.vcf.gz
md5sum: 9d491cfa84067450342ba8e66c75e5b8 md5sum: 9d491cfa84067450342ba8e66c75e5b8

8
tests/software/bcftools/isec/main.nf
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@ -6,10 +6,10 @@ include { BCFTOOLS_ISEC } from '../../../../software/bcftools/isec/main.nf' addP
workflow test_bcftools_isec { workflow test_bcftools_isec {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz", checkIfExists: true)], file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi", checkIfExists: true)] file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)]
] ]
BCFTOOLS_ISEC ( input ) BCFTOOLS_ISEC ( input )

12
tests/software/bcftools/isec/test.yml
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@ -1,18 +1,18 @@
- name: bcftools isec - name: bcftools isec test_bcftools_isec
command: nextflow run ./tests/software/bcftools/isec -entry test_bcftools_isec -c tests/config/nextflow.config command: nextflow run tests/software/bcftools/isec -entry test_bcftools_isec -c tests/config/nextflow.config
tags: tags:
- bcftools - bcftools
- bcftools_isec - bcftools_isec
files: files:
- path: output/bcftools/test/0000.vcf.gz - path: output/bcftools/test/0000.vcf.gz
md5sum: fc178eb342a91dc0d1d568601ad8f8e2 md5sum: fc178eb342a91dc0d1d568601ad8f8e2
- path: output/bcftools/test/0001.vcf.gz.tbi
md5sum: 36e11bf96ed0af4a92caa91a68612d64
- path: output/bcftools/test/sites.txt
md5sum: 1cea3fbde7f6d3c97f3d39036f9690df
- path: output/bcftools/test/0000.vcf.gz.tbi - path: output/bcftools/test/0000.vcf.gz.tbi
md5sum: 36e11bf96ed0af4a92caa91a68612d64 md5sum: 36e11bf96ed0af4a92caa91a68612d64
- path: output/bcftools/test/0001.vcf.gz - path: output/bcftools/test/0001.vcf.gz
md5sum: fc178eb342a91dc0d1d568601ad8f8e2 md5sum: fc178eb342a91dc0d1d568601ad8f8e2
- path: output/bcftools/test/0001.vcf.gz.tbi
md5sum: 36e11bf96ed0af4a92caa91a68612d64
- path: output/bcftools/test/README.txt - path: output/bcftools/test/README.txt
md5sum: 10fc33b66522645600d44afbd41fb792 md5sum: 10fc33b66522645600d44afbd41fb792
- path: output/bcftools/test/sites.txt
md5sum: 1cea3fbde7f6d3c97f3d39036f9690df

8
tests/software/bcftools/merge/main.nf
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@ -7,10 +7,10 @@ include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' ad
workflow test_bcftools_merge { workflow test_bcftools_merge {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz", checkIfExists: true) ], file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi", checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi", checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
] ]
BCFTOOLS_MERGE ( input ) BCFTOOLS_MERGE ( input )

6
tests/software/bcftools/merge/test.yml
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@ -1,8 +1,8 @@
- name: bcftools merge - name: bcftools merge test_bcftools_merge
command: nextflow run ./tests/software/bcftools/merge -entry test_bcftools_merge -c tests/config/nextflow.config command: nextflow run tests/software/bcftools/merge -entry test_bcftools_merge -c tests/config/nextflow.config
tags: tags:
- bcftools
- bcftools_merge - bcftools_merge
- bcftools
files: files:
- path: output/bcftools/test.vcf.gz - path: output/bcftools/test.vcf.gz
md5sum: 52165fc4149c61547e63800b876c9661 md5sum: 52165fc4149c61547e63800b876c9661

4
tests/software/bcftools/mpileup/main.nf
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@ -7,8 +7,8 @@ include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf
workflow test_bcftools_mpileup { workflow test_bcftools_mpileup {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // 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) ]
BCFTOOLS_MPILEUP ( input, fasta ) BCFTOOLS_MPILEUP ( input, fasta )
} }

14
tests/software/bcftools/mpileup/test.yml
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@ -1,12 +1,12 @@
- name: bcftools mpileup - name: bcftools mpileup test_bcftools_mpileup
command: nextflow run ./tests/software/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config command: nextflow run tests/software/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config
tags: tags:
- bcftools
- bcftools_mpileup - bcftools_mpileup
- bcftools
files: files:
- path: output/bcftools/test.vcf.gz
md5sum: 518f770a9d04004c4493fc2167280653
- path: output/bcftools/test.vcf.gz.tbi
md5sum: f4be4d707434b3b960fde100b7ec3bf3
- path: output/bcftools/test.bcftools_stats.txt - path: output/bcftools/test.bcftools_stats.txt
md5sum: 2d506e32837a53a01fea0fc90402632a md5sum: 2d506e32837a53a01fea0fc90402632a
- path: output/bcftools/test.vcf.gz.tbi
md5sum: 11d90b5b35e4adf6b44fc53bec93bed3
- path: output/bcftools/test.vcf.gz
md5sum: 2cf273a9fa3784383799b6b24df2f88c

2
tests/software/bcftools/stats/main.nf
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@ -6,7 +6,7 @@ include { BCFTOOLS_STATS } from '../../../../software/bcftools/stats/main.nf' ad
workflow test_bcftools_stats { workflow test_bcftools_stats {
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) ]
] ]
BCFTOOLS_STATS ( input ) BCFTOOLS_STATS ( input )

4
tests/software/bcftools/stats/test.yml
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@ -1,5 +1,5 @@
- name: bcftools stats - name: bcftools stats test_bcftools_stats
command: nextflow run ./tests/software/bcftools/stats -entry test_bcftools_stats -c tests/config/nextflow.config command: nextflow run tests/software/bcftools/stats -entry test_bcftools_stats -c tests/config/nextflow.config
tags: tags:
- bcftools - bcftools
- bcftools_stats - bcftools_stats

14
tests/software/gatk4/variantfiltration/main.nf
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@ -2,17 +2,17 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"'] test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"', 'suffix': '.filtered']
include { GATK4_VARIANTFILTRATION } from '../../../../software/gatk4/variantfiltration/main.nf' addParams( options: test_options ) include { GATK4_VARIANTFILTRATION } from '../../../../software/gatk4/variantfiltration/main.nf' addParams( options: test_options )
workflow test_gatk4_variantfiltration { workflow test_gatk4_variantfiltration {
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) ]
]
fasta = [ file("tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true),
file("tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true),
file("tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
] ]
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
fai = [ file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
genome_dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
GATK4_VARIANTFILTRATION ( input, fasta )
GATK4_VARIANTFILTRATION ( input, fasta, fai, genome_dict )
} }

9
tests/software/gatk4/variantfiltration/test.yml
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@ -1,8 +1,9 @@
- name: Run tests for gatk4/variantfiltration - test_gatk4_variantfiltration - name: gatk4 variantfiltration test_gatk4_variantfiltration
command: nextflow run tests/software/gatk4/variantfiltration -entry test_gatk4_variantfiltration command: nextflow run tests/software/gatk4/variantfiltration -entry test_gatk4_variantfiltration -c tests/config/nextflow.config
-c tests/config/nextflow.config
tags: tags:
- gatk4
- gatk4_variantfiltration - gatk4_variantfiltration
- gatk4
files: files:
- path: output/gatk4/test.filtered.vcf - path: output/gatk4/test.filtered.vcf
contains:
- "AC=2;AN=2;DP=1;DP4=0,0,1,0;MQ=60;MQ0F=0;SGB=-0.379885"