Fix more version commands (#750)

* Fix outstanding tests

* Fix more version commands

* Fix remaining modules
This commit is contained in:
Harshil Patel 2021-09-28 06:56:27 +01:00 committed by GitHub
parent 43c2779258
commit 3c5492b4a3
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
39 changed files with 185 additions and 157 deletions

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@ -35,7 +35,7 @@ process BISMARK_SUMMARY {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
END_VERSIONS
"""
}

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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
params.options = [:]
options = initOptions(params.options)
def VERSION = 0.1 // No version information printed
def VERSION = '0.1' // No version information printed
process CHROMAP_CHROMAP {
tag "$meta.id"

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@ -43,7 +43,7 @@ process GRAPHMAP2_ALIGN {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
"""
}

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@ -36,7 +36,7 @@ process GRAPHMAP2_INDEX {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(graphmap2 align 2>&1 | sed 's/^.*Version: v//; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
"""
}

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@ -29,10 +29,14 @@ process GUNZIP {
def software = getSoftwareName(task.process)
gunzip = archive.toString() - '.gz'
"""
gunzip -f $options.args $archive
gunzip \\
-f \\
$options.args \\
$archive
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(gunzip --version 2>&1 | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}

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@ -44,7 +44,7 @@ process IVAR_CONSENSUS {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -40,7 +40,7 @@ process IVAR_TRIM {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -47,7 +47,7 @@ process IVAR_VARIANTS {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(ivar version 2>&1 | sed 's/^.*iVar version //; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -50,7 +50,7 @@ process KRAKEN2_KRAKEN2 {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(kraken2 --version 2>&1 | sed 's/^.*Kraken version //; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -39,7 +39,7 @@ process LOFREQ_CALL {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}

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@ -41,7 +41,7 @@ process LOFREQ_CALLPARALLEL {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}

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@ -37,7 +37,7 @@ process LOFREQ_FILTER {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^version: //; s/ *commit.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}

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@ -37,7 +37,7 @@ process LOFREQ_INDELQUAL {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(lofreq version 2>&1 | sed 's/^.*lofreq //; s/Using.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}

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@ -40,7 +40,7 @@ process MINIA {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(minia --version 2>&1 | sed 's/^.*Minia version //; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(minia --version 2>&1) | sed 's/^.*Minia version //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -42,7 +42,7 @@ process PRESEQ_LCEXTRAP {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(preseq 2>&1 | sed 's/^.*Version: //; s/Usage:.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
END_VERSIONS
"""
}

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@ -58,7 +58,7 @@ process QUALIMAP_BAMQC {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(qualimap 2>&1 | sed 's/^.*QualiMap v.//; s/Built.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
}

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@ -33,7 +33,7 @@ process TABIX_BGZIP {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -34,7 +34,7 @@ process TABIX_BGZIPTABIX {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -32,7 +32,7 @@ process TABIX_TABIX {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(tabix -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}

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@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
params.options = [:]
options = initOptions(params.options)
def VERSION = '377' // No version information printed
process UCSC_WIGTOBIGWIG {
tag '$wig'
label 'process_medium'
@ -38,7 +40,7 @@ process UCSC_WIGTOBIGWIG {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(wigToBigWig 2>&1 | sed 's/wigToBigWig v //; s/ - Convert.*\$//')
${getSoftwareName(task.process)}: \$(echo "$VERSION")
END_VERSIONS
"""
}

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@ -22,17 +22,21 @@ process UNTAR {
path archive
output:
path "$untar" , emit: untar
path "versions.yml" , emit: version
path "$untar" , emit: untar
path "versions.yml", emit: version
script:
def software = getSoftwareName(task.process)
untar = archive.toString() - '.tar.gz'
"""
tar -xzvf $options.args $archive
tar \\
-xzvf \\
$options.args \\
$archive
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(tar --version 2>&1 | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}

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@ -40,7 +40,7 @@ process UNZIP {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
7za: \$( 7za --help) grep Version | sed 's/.*p7zip Version//; s/(.*//' )
7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
END_VERSIONS
"""
}

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@ -3,18 +3,23 @@
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' addParams( options: [:] )
workflow test_bwa_sampe {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
Channel
.fromList(
[
[ id:'test', single_end:false ],
[ [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
]
).collect()
.set { input }
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
BWA_ALN ( input, BWA_INDEX.out.index )
BWA_SAMPE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
BWA_SAMPE ( input.join(BWA_ALN.out.sai), BWA_INDEX.out.index )
}

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@ -3,17 +3,20 @@
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
include { BWA_SAMSE } from '../../../../modules/bwa/samse/main.nf' addParams( options: [:] )
workflow test_bwa_samse {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
Channel
.fromList(
[ [ id:'test', single_end:true ],
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
).collect()
.set { input }
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
BWA_ALN ( input, BWA_INDEX.out.index )
BWA_SAMSE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
BWA_SAMSE ( input.join(BWA_ALN.out.sai, by:[0]), BWA_INDEX.out.index )
}

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@ -2,9 +2,8 @@
nextflow.enable.dsl = 2
include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf' addParams( options: [:] )
//
// Test with single-end data
@ -16,7 +15,7 @@ workflow test_bwameth_align_single_end {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMETH_INDEX ( fasta )
BWAMETH_ALIGN_SE ( input, BWAMETH_INDEX.out.index )
BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
}
//
@ -30,5 +29,5 @@ workflow test_bwameth_align_paired_end {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMETH_INDEX ( fasta )
BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index )
BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
}

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@ -4,7 +4,7 @@
- bwameth
- bwameth/align
files:
- path: output/test_single_end/test.bam
- path: output/bwameth/test.bam
- name: bwameth align paired-end test workflow
command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
@ -12,5 +12,5 @@
- bwameth
- bwameth/align
files:
- path: output/test_paired_end/test.bam
- path: output/bwameth/test.bam

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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [:] )
include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [publish_dir:'genmap'] )
workflow test_genmap_index {

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@ -4,45 +4,45 @@
- genmap
- genmap/index
files:
- path: output/index/genmap/index.ids.concat
- path: output/genmap/genmap/index.ids.concat
md5sum: da6caa25f62c5407ccdfbcce1fa92408
- path: output/index/genmap/index.ids.limits
- path: output/genmap/genmap/index.ids.limits
md5sum: f82636c5da188aec131d3a809473eff1
- path: output/index/genmap/index.info.concat
- path: output/genmap/genmap/index.info.concat
md5sum: 8ba5273aa9e58722bf45b9cc39fc6bfe
- path: output/index/genmap/index.info.limits
- path: output/genmap/genmap/index.info.limits
md5sum: 3522f2811f4ddf04598809fc84a1459e
- path: output/index/genmap/index.lf.drp
- path: output/genmap/genmap/index.lf.drp
md5sum: dd85d6a23af2c7adf2695658e3056c08
- path: output/index/genmap/index.lf.drp.sbl
- path: output/genmap/genmap/index.lf.drp.sbl
md5sum: f1d3ff8443297732862df21dc4e57262
- path: output/index/genmap/index.lf.drs
- path: output/genmap/genmap/index.lf.drs
md5sum: 93b885adfe0da089cdf634904fd59f71
- path: output/index/genmap/index.lf.drv
- path: output/genmap/genmap/index.lf.drv
md5sum: e06b605496bd91b32afa3c4f56d934ac
- path: output/index/genmap/index.lf.drv.sbl
- path: output/genmap/genmap/index.lf.drv.sbl
md5sum: 8dd6bb7329a71449b0a1b292b5999164
- path: output/index/genmap/index.lf.pst
- path: output/genmap/genmap/index.lf.pst
md5sum: e8daba34298e99e42942435286f9b3f0
- path: output/index/genmap/index.rev.lf.drp
- path: output/genmap/genmap/index.rev.lf.drp
md5sum: 5d9107e3aeec0721553dd661d4365fef
- path: output/index/genmap/index.rev.lf.drp.sbl
- path: output/genmap/genmap/index.rev.lf.drp.sbl
md5sum: f1d3ff8443297732862df21dc4e57262
- path: output/index/genmap/index.rev.lf.drs
- path: output/genmap/genmap/index.rev.lf.drs
md5sum: 93b885adfe0da089cdf634904fd59f71
- path: output/index/genmap/index.rev.lf.drv
- path: output/genmap/genmap/index.rev.lf.drv
md5sum: df7e795edc0a034577a9d2599fe8cfeb
- path: output/index/genmap/index.rev.lf.drv.sbl
- path: output/genmap/genmap/index.rev.lf.drv.sbl
md5sum: 8dd6bb7329a71449b0a1b292b5999164
- path: output/index/genmap/index.rev.lf.pst
- path: output/genmap/genmap/index.rev.lf.pst
md5sum: e8daba34298e99e42942435286f9b3f0
- path: output/index/genmap/index.sa.ind
- path: output/genmap/genmap/index.sa.ind
md5sum: e21e5c7ce887cc8e3d0fa44ab1019cab
- path: output/index/genmap/index.sa.len
- path: output/genmap/genmap/index.sa.len
md5sum: 5dfc20cfe8ed9892451461a8d402f51c
- path: output/index/genmap/index.sa.val
- path: output/genmap/genmap/index.sa.val
md5sum: 400ee7f2fe93b2000ae3a5da5e509730
- path: output/index/genmap/index.txt.concat
- path: output/genmap/genmap/index.txt.concat
md5sum: b4303962e0c176107945f3405370e6ae
- path: output/index/genmap/index.txt.limits
- path: output/genmap/genmap/index.txt.limits
md5sum: 4480a068db603e4c9a27bc4fa9ceaf14

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@ -5,4 +5,4 @@
- ivar/trim
files:
- path: output/ivar/test.bam
md5sum: 8705d032b28a1c3dbfe78fa762a2132f
md5sum: 12cff17d43b1efdba8120a6bff5311e3

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@ -6,7 +6,7 @@
files:
- path: ./output/qualimap/test/qualimapReport.html
- path: ./output/qualimap/test/genome_results.txt
md5sum: 00ad697dbec5141428ac8d850c13e1c5
md5sum: 5ec87ea86ad734d512c8c76fe8eb37b1
- path: ./output/qualimap/test/css/plus.png
md5sum: 0125e6faa04e2cf0141a2d599d3bb220
- path: ./output/qualimap/test/css/down-pressed.png

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@ -2,20 +2,21 @@
nextflow.enable.dsl = 2
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
workflow test_rsem_calculateexpression {
input = [
[ id:'test', single_end:false, strandedness: 'forward' ], // meta map
[
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
input = [ [ id:'test', single_end:false, strandedness: 'forward' ], // meta map
[file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)]
]
RSEM_PREPAREREFERENCE ( fasta, gtf )
RSEM_CALCULATEEXPRESSION( input, RSEM_PREPAREREFERENCE.out.index )
}

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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [:])
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [publish_dir:'rsem'])
workflow test_rsem_preparereference {

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@ -4,19 +4,19 @@
- rsem
- rsem/preparereference
files:
- path: output/index/rsem/genome.chrlist
- path: output/rsem/rsem/genome.chrlist
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/index/rsem/genome.fasta
- path: output/rsem/rsem/genome.fasta
md5sum: f315020d899597c1b57e5fe9f60f4c3e
- path: output/index/rsem/genome.grp
- path: output/rsem/rsem/genome.grp
md5sum: c2848a8b6d495956c11ec53efc1de67e
- path: output/index/rsem/genome.idx.fa
- path: output/rsem/rsem/genome.idx.fa
md5sum: 050c521a2719c2ae48267c1e65218f29
- path: output/index/rsem/genome.n2g.idx.fa
- path: output/rsem/rsem/genome.n2g.idx.fa
md5sum: 050c521a2719c2ae48267c1e65218f29
- path: output/index/rsem/genome.seq
- path: output/rsem/rsem/genome.seq
md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
- path: output/index/rsem/genome.ti
- path: output/rsem/rsem/genome.ti
md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
- path: output/index/rsem/genome.transcripts.fa
- path: output/rsem/rsem/genome.transcripts.fa
md5sum: 050c521a2719c2ae48267c1e65218f29

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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [:] )
include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [publish_dir:'star'] )
workflow test_star_genomegenerate {
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

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@ -4,34 +4,34 @@
- star/genomegenerate
- star
files:
- path: output/index/star/Genome
- path: output/star/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- path: output/index/star/Log.out
- path: output/index/star/SA
- path: output/star/star/Log.out
- path: output/star/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- path: output/index/star/SAindex
- path: output/star/star/SAindex
md5sum: d0fbf2789ee1e9f60c352ba3655d9de4
- path: output/index/star/chrLength.txt
- path: output/star/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/index/star/chrName.txt
- path: output/star/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/index/star/chrNameLength.txt
- path: output/star/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/index/star/chrStart.txt
- path: output/star/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- path: output/index/star/exonGeTrInfo.tab
- path: output/star/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- path: output/index/star/exonInfo.tab
- path: output/star/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- path: output/index/star/geneInfo.tab
- path: output/star/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- path: output/index/star/genomeParameters.txt
- path: output/star/star/genomeParameters.txt
md5sum: 5a1ec027e575c3d7c1851e6b80fb8c5d
- path: output/index/star/sjdbInfo.txt
- path: output/star/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/index/star/sjdbList.fromGTF.out.tab
- path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- path: output/index/star/sjdbList.out.tab
- path: output/star/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- path: output/index/star/transcriptInfo.tab
- path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36

View file

@ -2,37 +2,45 @@
nextflow.enable.dsl = 2
include { STRINGTIE as STRINGTIE_FORWARD } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
include { STRINGTIE as STRINGTIE_REVERSE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
include { STRINGTIE_MERGE as STRINGTIE_FORWARD_MERGE} from '../../../../modules/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward_merge'] )
include { STRINGTIE_MERGE as STRINGTIE_REVERSE_MERGE} from '../../../../modules/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse_merge'] )
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' addParams( options: [:] )
/*
* Test with forward strandedness
*/
workflow test_stringtie_forward_merge {
input = [ [ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_FORWARD ( input, annotation_gtf )
STRINGTIE_FORWARD.out.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_FORWARD_MERGE ( stringtie_gtf, annotation_gtf )
input = [
[ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE
.out
.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
}
/*
* Test with reverse strandedness
*/
workflow test_stringtie_reverse_merge {
input = [ [ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_REVERSE ( input, annotation_gtf )
STRINGTIE_REVERSE.out.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_REVERSE_MERGE ( stringtie_gtf, annotation_gtf )
input = [
[ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE
.out
.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
}

View file

@ -1,22 +1,22 @@
- name: stringtie forward-strand merge
- name: stringtie merge forward-strand
command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_forward_merge -c tests/config/nextflow.config
tags:
- stringtie
- stringtie/merge
files:
- path: ./output/test_stringtie_forward_merge/stringtie.merged.gtf
- path: ./output/stringtie/stringtie.merged.gtf
contains:
- 'stringtie'
- 'merge'
- 'chr22'
- name: stringtie reverse-strand merge
- name: stringtie merge reverse-strand
command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
tags:
- stringtie
- stringtie/merge
files:
- path: ./output/test_stringtie_reverse_merge/stringtie.merged.gtf
- path: ./output/stringtie/stringtie.merged.gtf
contains:
- 'stringtie'
- 'merge'

View file

@ -2,27 +2,29 @@
nextflow.enable.dsl = 2
include { STRINGTIE as STRINGTIE_FORWARD } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
include { STRINGTIE as STRINGTIE_REVERSE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
//
// Test with forward strandedness
//
workflow test_stringtie_forward {
input = [ [ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
input = [
[ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_FORWARD ( input, annotation_gtf )
STRINGTIE ( input, annotation_gtf )
}
//
// Test with reverse strandedness
//
workflow test_stringtie_reverse {
input = [ [ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
input = [
[ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_REVERSE ( input, annotation_gtf )
STRINGTIE ( input, annotation_gtf )
}

View file

@ -1,43 +1,43 @@
- name: test_stringtie_forward
- name: stringtie stringtie forward
command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
tags:
- stringtie
- stringtie/stringtie
files:
- path: ./output/test_stringtie_forward/test.transcripts.gtf
- path: ./output/test_stringtie_forward/test.gene.abundance.txt
- path: ./output/stringtie/test.transcripts.gtf
- path: ./output/stringtie/test.gene.abundance.txt
md5sum: 7d8bce7f2a922e367cedccae7267c22e
- path: ./output/test_stringtie_forward/test.coverage.gtf
- path: ./output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/test_stringtie_forward/test.ballgown/e_data.ctab
- path: ./output/stringtie/test.ballgown/e_data.ctab
md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
- path: ./output/test_stringtie_forward/test.ballgown/i_data.ctab
- path: ./output/stringtie/test.ballgown/i_data.ctab
md5sum: be3abe09740603213f83d50dcf81427f
- path: ./output/test_stringtie_forward/test.ballgown/t_data.ctab
- path: ./output/stringtie/test.ballgown/t_data.ctab
md5sum: 3b66c065da73ae0dd41cc332eff6a818
- path: ./output/test_stringtie_forward/test.ballgown/i2t.ctab
- path: ./output/stringtie/test.ballgown/i2t.ctab
md5sum: 8a117c8aa4334b4c2d4711932b006fb4
- path: ./output/test_stringtie_forward/test.ballgown/e2t.ctab
- path: ./output/stringtie/test.ballgown/e2t.ctab
md5sum: e981c0038295ae54b63cedb1083f1540
- name: test_stringtie_reverse
- name: stringtie stringtie reverse
command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
tags:
- stringtie
- stringtie/stringtie
files:
- path: ./output/test_stringtie_reverse/test.transcripts.gtf
- path: ./output/test_stringtie_reverse/test.gene.abundance.txt
- path: ./output/stringtie/test.transcripts.gtf
- path: ./output/stringtie/test.gene.abundance.txt
md5sum: 7385b870b955dae2c2ab78a70cf05cce
- path: ./output/test_stringtie_reverse/test.coverage.gtf
- path: ./output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/test_stringtie_reverse/test.ballgown/e_data.ctab
- path: ./output/stringtie/test.ballgown/e_data.ctab
md5sum: 879b6696029d19c4737b562e9d149218
- path: ./output/test_stringtie_reverse/test.ballgown/i_data.ctab
- path: ./output/stringtie/test.ballgown/i_data.ctab
md5sum: be3abe09740603213f83d50dcf81427f
- path: ./output/test_stringtie_reverse/test.ballgown/t_data.ctab
- path: ./output/stringtie/test.ballgown/t_data.ctab
md5sum: 3b66c065da73ae0dd41cc332eff6a818
- path: ./output/test_stringtie_reverse/test.ballgown/i2t.ctab
- path: ./output/stringtie/test.ballgown/i2t.ctab
md5sum: 8a117c8aa4334b4c2d4711932b006fb4
- path: ./output/test_stringtie_reverse/test.ballgown/e2t.ctab
- path: ./output/stringtie/test.ballgown/e2t.ctab
md5sum: e981c0038295ae54b63cedb1083f1540