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Update and check tests are running for all modules (#420)

Browse source 
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
This commit is contained in:
Harshil Patel 2021-04-09 13:47:05 +01:00 committed by GitHub
parent 5a59e61052
commit 5e18e36895
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
29 changed files with 68 additions and 68 deletions
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10
tests/config/pytest_software.yml
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@ -450,14 +450,6 @@ seqkit/split2:
- software/seqkit/split2/**
- tests/software/seqkit/split2/**
sequenza/bam2seqz:
- software/sequenza/bam2seqz/**
- tests/software/sequenza/bam2seqz/**
sequenza/wiggle:
- software/sequenza/wiggle/**
- tests/software/sequenza/wiggle/**
sequenzautils/bam2seqz:
- software/sequenzautils/bam2seqz/**
- tests/software/sequenzautils/bam2seqz/**
@ -538,7 +530,7 @@ vcftools:
- software/vcftools/**
- tests/software/vcftools/**
yara:
yara/mapper:
- software/yara/mapper/**
- tests/software/yara/mapper/**

5
tests/config/test_data.config
View file

@ -28,7 +28,7 @@ params {
all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
contigs_fasta = "${test_data_dir}/genomics/sarscov2/genome/contigs.fasta"
}
'illumina' {
@ -50,6 +50,9 @@ params {
test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz"
test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz"
test_bedgraph = "${test_data_dir}/genomics/sarscov2/illumina/bedgraph/test.bedgraph"
test_wig_gz = "${test_data_dir}/genomics/sarscov2/illumina/wig/test.wig.gz"
test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"

4
tests/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph Normal file
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@ -0,0 +1,4 @@
MT192765.1 1242 1264 1
MT192765.1 1573 1595 0.3
MT192765.1 1623 1651 1
MT192765.1 1942 1964 0.2

0
tests/data/genomics/sarscov2/genome/gcwiggle/test.wig.gz → tests/data/genomics/sarscov2/illumina/wig/test.wig.gz
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6
tests/software/bowtie/align/main.nf
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@ -17,10 +17,10 @@ workflow test_bowtie_align_single_end {
workflow test_bowtie_align_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) ]
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE_BUILD ( fasta )
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )

24
tests/software/bowtie/align/test.yml
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@ -8,17 +8,17 @@
- path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out
md5sum: 4b9140ceadb8a18ae9330885370f8a0b
- path: ./output/index/bowtie/test_genome.3.ebwt
- path: ./output/index/bowtie/genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/index/bowtie/test_genome.2.ebwt
- path: ./output/index/bowtie/genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- path: ./output/index/bowtie/test_genome.rev.2.ebwt
- path: ./output/index/bowtie/genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- path: ./output/index/bowtie/test_genome.4.ebwt
- path: ./output/index/bowtie/genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/index/bowtie/test_genome.rev.1.ebwt
- path: ./output/index/bowtie/genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06
- path: ./output/index/bowtie/test_genome.1.ebwt
- path: ./output/index/bowtie/genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199
- name: bowtie align paired-end
@ -30,15 +30,15 @@
files:
- path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out
- path: ./output/index/bowtie/test_genome.3.ebwt
- path: ./output/index/bowtie/genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/index/bowtie/test_genome.2.ebwt
- path: ./output/index/bowtie/genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- path: ./output/index/bowtie/test_genome.rev.2.ebwt
- path: ./output/index/bowtie/genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- path: ./output/index/bowtie/test_genome.4.ebwt
- path: ./output/index/bowtie/genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/index/bowtie/test_genome.rev.1.ebwt
- path: ./output/index/bowtie/genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06
- path: ./output/index/bowtie/test_genome.1.ebwt
- path: ./output/index/bowtie/genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199

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

12
tests/software/bowtie/build_test/test.yml
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@ -4,15 +4,15 @@
- bowtie
- bowtie/build
files:
- path: ./output/index/bowtie/test_genome.3.ebwt
- path: ./output/index/bowtie/genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/index/bowtie/test_genome.2.ebwt
- path: ./output/index/bowtie/genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- path: ./output/index/bowtie/test_genome.rev.2.ebwt
- path: ./output/index/bowtie/genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- path: ./output/index/bowtie/test_genome.4.ebwt
- path: ./output/index/bowtie/genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/index/bowtie/test_genome.rev.1.ebwt
- path: ./output/index/bowtie/genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06
- path: ./output/index/bowtie/test_genome.1.ebwt
- path: ./output/index/bowtie/genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199

2
tests/software/fgbio/callmolecularconsensusreads/test.yml
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@ -1,8 +1,8 @@
- name: fgbio callmolecularconsensusreads
command: nextflow run tests/software/fgbio/callmolecularconsensusreads -entry test_fgbio_callmolecularconsensusreads -c tests/config/nextflow.config
tags:
- fgbio_callmolecularconsensusreads
- fgbio
- fgbio/callmolecularconsensusreads
files:
- path: output/fgbio/test_molreads.bam
md5sum: 7010bcdc037c36af13dbc370c06c76d3

2
tests/software/fgbio/sortbam/test.yml
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@ -1,8 +1,8 @@
- name: fgbio sortbam
command: nextflow run tests/software/fgbio/sortbam -entry test_fgbio_sortbam -c tests/config/nextflow.config
tags:
- fgbio_sortbam
- fgbio
- fgbio/sortbam
files:
- path: output/fgbio/test.bam
md5sum: 56987f74214cdc72ae840e0007ff4935

2
tests/software/gatk4/createsequencedictionary/test.yml
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@ -2,7 +2,7 @@
command: nextflow run tests/software/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_createsequencedictionary
- gatk4/createsequencedictionary
files:
- path: output/gatk4/genome.dict
md5sum: 7362679f176e0f52add03c08f457f646

2
tests/software/gatk4/haplotypecaller/test.yml
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@ -1,8 +1,8 @@
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller
command: nextflow run tests/software/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c tests/config/nextflow.config
tags:
- gatk4_haplotypecaller
- gatk4
- gatk4/haplotypecaller
files:
- path: output/gatk4/test.vcf.gz
should_exist: true

2
tests/software/gatk4/markduplicates/test.yml
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@ -2,7 +2,7 @@
command: nextflow run tests/software/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_markduplicates
- gatk4/markduplicates
files:
- path: output/gatk4/test.bam
md5sum: b58d47345e3ce5825c0641c9d6e6cb7a

8
tests/software/hisat2/align/test.yml
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@ -1,9 +1,9 @@
- name: hisat2 align test_hisat2_align_single_end
command: nextflow run tests/software/hisat2/align -entry test_hisat2_align_single_end -c tests/config/nextflow.config
tags:
- hisat2_align_single_end
- hisat2_align
- hisat2
- hisat2/align
- hisat2_align_single_end
files:
- path: output/hisat2/test.hisat2.summary.log
md5sum: 7b8a9e61b7646da1089b041333c41a87
@ -30,9 +30,9 @@
- name: hisat2 align test_hisat2_align_paired_end
command: nextflow run tests/software/hisat2/align -entry test_hisat2_align_paired_end -c tests/config/nextflow.config
tags:
- hisat2_align_paired_end
- hisat2_align
- hisat2
- hisat2/align
- hisat2_align_paired_end
files:
- path: output/hisat2/test.hisat2.summary.log
md5sum: 9839b31db795958cc4b70711a3414e9c

2
tests/software/hisat2/build_test/test.yml
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@ -2,7 +2,7 @@
command: nextflow run tests/software/hisat2/build_test -entry test_hisat2_build -c tests/config/nextflow.config
tags:
- hisat2
- hisat2_build
- hisat2/build
files:
- path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e

2
tests/software/hisat2/extractsplicesites/test.yml
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@ -2,7 +2,7 @@
command: nextflow run tests/software/hisat2/extractsplicesites -entry test_hisat2_extractsplicesites -c tests/config/nextflow.config
tags:
- hisat2
- hisat2_extractsplicesites
- hisat2/extractsplicesites
files:
- path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e

4
tests/software/minimap2/align/main.nf
View file

@ -15,8 +15,8 @@ workflow test_minimap2_align_single_end {
workflow test_minimap2_align_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) ]
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)

2
tests/software/msisensor/msi/test.yml
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@ -2,7 +2,7 @@
command: nextflow run ./tests/software/msisensor/msi -entry test_msisensor_msi -c tests/config/nextflow.config
tags:
- msisensor
- msisensor_msi
- msisensor/msi
files:
- path: output/msisensor/test
md5sum: a3290f7539dbbf83777e8590156c0e28

2
tests/software/msisensor/scan/test.yml
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@ -2,7 +2,7 @@
command: nextflow run ./tests/software/msisensor/scan -entry test_msisensor_scan -c tests/config/nextflow.config
tags:
- msisensor
- msisensor_scan
- msisensor/scan
files:
- path: output/msisensor/test.msisensor_scan.tab
md5sum: b7ae85acdcfc1a51e867ab3446d6fb59

2
tests/software/picard/collectmultiplemetrics/test.yml
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@ -2,7 +2,7 @@
command: nextflow run ./tests/software/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
tags:
- picard
- picard_collectmultiplemetrics
- picard/collectmultiplemetrics
files:
# These can't be md5'd consistently
- path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics

8
tests/software/sequenzautils/bam2seqz/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../software/sequenzautils/bam2seqz/main.nf' addParams( options: [:] )
workflow test_sequenzautils_bam2seqz {
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)
@ -13,8 +13,8 @@ workflow test_sequenzautils_bam2seqz {
tumourbam,
normalbam
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
wigfile = file(params.test_data['sarscov2']['genome']['test_wig_gz'], checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
wig = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true)
SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wigfile )
SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wig )
}

3
tests/software/sequenzautils/bam2seqz/test.yml
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@ -2,6 +2,7 @@
command: nextflow run ./tests/software/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c tests/config/nextflow.config
tags:
- sequenzautils
- sequenzautils_bam2seqz
- sequenzautils/bam2seqz
files:
- path: output/sequenzautils/test.seqz.gz
md5sum: 12b41979a498ac10c0aff162b12e6a6e

2
tests/software/sequenzautils/gcwiggle/test.yml
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@ -4,6 +4,6 @@
command: nextflow run ./tests/software/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c tests/config/nextflow.config
tags:
- sequenzautils
- sequenzautils_gcwiggle
- sequenzautils/gcwiggle
files:
- path: output/sequenzautils/test.wig.gz

8
tests/software/stringtie/main.nf
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@ -10,8 +10,8 @@ include { STRINGTIE as STRINGTIE_REVERSE } from '../../../software/stringtie/mai
*/
workflow test_stringtie_forward {
input = [ [ id:'test', strandedness:'forward' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ] ]
gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_FORWARD ( input, gtf )
}
@ -21,9 +21,9 @@ workflow test_stringtie_forward {
*/
workflow test_stringtie_reverse {
input = [ [ id:'test', strandedness:'reverse' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_REVERSE ( input, gtf )
}

4
tests/software/stringtie/test.yml
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@ -4,7 +4,7 @@
- stringtie
files:
- path: ./output/test_stringtie_forward/test.transcripts.gtf
md5sum: cbce87f06598eb756e7670ba3217a42f
md5sum: 8abb6a87581bd7a61af74085b5a6daec
- path: ./output/test_stringtie_forward/test.gene.abundance.txt
md5sum: 7d8bce7f2a922e367cedccae7267c22e
- path: ./output/test_stringtie_forward/test.coverage.gtf
@ -26,7 +26,7 @@
- stringtie
files:
- path: ./output/test_stringtie_reverse/test.transcripts.gtf
md5sum: bb992085e42bad19877c847dae496c80
md5sum: 8bdcda06f39183fa4312644bd0e41bb5
- path: ./output/test_stringtie_reverse/test.gene.abundance.txt
md5sum: 7385b870b955dae2c2ab78a70cf05cce
- path: ./output/test_stringtie_reverse/test.coverage.gtf

6
tests/software/subread/featurecounts/test.yml
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@ -2,8 +2,8 @@
command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_forward -c tests/config/nextflow.config
tags:
- subread
- subread/featurecounts
- subread_featurecounts_forward
- subread_featurecounts
files:
- path: output/subread/test.featureCounts.txt.summary
md5sum: d78617192451a57f6ef249ddcaf13720
@ -14,7 +14,7 @@
command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config
tags:
- subread
- subread_featurecounts
- subread/featurecounts
- subread_featurecounts_reverse
files:
- path: output/subread/test.featureCounts.txt.summary
@ -26,7 +26,7 @@
command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config
tags:
- subread
- subread_featurecounts
- subread/featurecounts
- subread_featurecounts_unstranded
files:
- path: output/subread/test.featureCounts.txt.summary

4
tests/software/ucsc/bed12tobigbed/main.nf
View file

@ -6,9 +6,9 @@ include { UCSC_BED12TOBIGBED } from '../../../../software/ucsc/bed12tobigbed/mai
workflow test_ucsc_bed12tobigbed {
input = [ [ id: 'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true ) ]
[ file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true ) ]
]
sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
UCSC_BED12TOBIGBED ( input, sizes )
}

4
tests/software/ucsc/bedgraphtobigwig/main.nf
View file

@ -6,9 +6,9 @@ include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../software/ucsc/bedgraphtobig
workflow test_ucsc_bedgraphtobigwig {
input = [ [ id:'test' ], // meta map
[ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true) ]
]
sizes = file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true)
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
UCSC_BEDGRAPHTOBIGWIG ( input, sizes )
}

2
tests/software/ucsc/bedgraphtobigwig/test.yml
View file

@ -4,4 +4,4 @@
- ucsc/bedgraphtobigwig
files:
- path: output/ucsc/test.bigWig
md5sum: 5346de25b01ecbff91b63178b3bfbeec
md5sum: 910ecc7f57e3bbd5fac5a8edba4f615d