kfukuta/wf-transcriptomes-v202
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de_analysis include in sample cmd

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Sarah Griffiths 2023-12-08 09:32:07 +00:00
parent 1a62c724b3
commit 3acf993586
3 changed files with 5 additions and 2 deletions
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2
CHANGELOG.md
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@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Memory requirements for each process. - Memory requirements for each process.
### Changed ### Changed
- Documentation. - Documentation.
### Fixed
- When Jaffa is run only output one report.
## [v0.4.2] ## [v0.4.2]
### Changed ### Changed

4
main.nf
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@ -606,8 +606,8 @@ workflow pipeline {
} }
if (jaffal_refBase){ if (jaffal_refBase){
gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation) gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation)
jaffal_out = gene_fusions.out.results_csv.collectFile(keepHeader: true, name: 'jaffal.csv') jaffal_out = gene_fusions.out.results_csv.map{ alias, csv -> csv}.collectFile(keepHeader: true, name: 'jaffal.csv')
}else{ } else{
jaffal_out = file("$projectDir/data/OPTIONAL_FILE") jaffal_out = file("$projectDir/data/OPTIONAL_FILE")
} }

1
nextflow.config
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@ -98,6 +98,7 @@ params {
"--minimap2_index_opts '-k15'", "--minimap2_index_opts '-k15'",
"--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'", "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
"--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'", "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
"--de_analysis",
] ]
agent = null agent = null
container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867" container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"