Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

FIX: Keep only one samplesheetToList #1406

Merged
merged 4 commits into from
Oct 11, 2024
Merged

FIX: Keep only one samplesheetToList #1406

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d40e650
only one samplesheetToList
maxulysse Oct 11, 2024
3989b24
update CHANGELOG
maxulysse Oct 11, 2024
bf0a3c1
Merge branch 'dev' into improve_samplesheetToList
maxulysse Oct 11, 2024
141c15a
Merge branch 'dev' into improve_samplesheetToList
maxulysse Oct 11, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ Special thanks to the following for their contributions to the release:

- [PR #1398](https://github.com/nf-core/rnaseq/pull/1398) - Bump pipeline version to 3.17.0dev
- [PR #1401](https://github.com/nf-core/rnaseq/pull/1401) - Template update for nf-core/tools v3.0.1
- [PR #1406](https://github.com/nf-core/rnaseq/pull/1406) - Keep only one samplesheetToList

### Parameters

Expand Down
22 changes: 0 additions & 22 deletions subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@ import groovy.json.JsonSlurper

include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
include { paramsSummaryMap } from 'plugin/nf-schema'
include { samplesheetToList } from 'plugin/nf-schema'
include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
Expand Down Expand Up @@ -71,28 +70,7 @@ workflow PIPELINE_INITIALISATION {
//
validateInputParameters()

//
// Create channel from input file provided through params.input
//

Channel
.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
.map {
meta, fastq_1, fastq_2 ->
if (!fastq_2) {
return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
} else {
return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
}
}
.groupTuple()
.map {
checkSamplesAfterGrouping(it)
}
.set{ ch_samplesheet }

emit:
samplesheet = ch_samplesheet
versions = ch_versions
}

Expand Down
6 changes: 3 additions & 3 deletions workflows/rnaseq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -121,10 +121,10 @@ workflow RNASEQ {
}
}
.groupTuple()
.map {
checkSamplesAfterGrouping(it)
.map { samplesheet ->
checkSamplesAfterGrouping(samplesheet)
}
.set{ ch_fastq }
.set { ch_fastq }

//
// Run RNA-seq FASTQ preprocessing subworkflow
Expand Down
Loading