Skip to content

Fix GFFREAD when gff file provided by user (add empty map to channel) @JoseEspinosa #444

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

Merged
JoseEspinosa merged 1 commit into from
Dec 24, 2024
Merged

Fix GFFREAD when gff file provided by user (add empty map to channel) @JoseEspinosa #444

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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 @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
- [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
- [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.

### Parameters

Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/prepare_genome.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,9 +71,9 @@ workflow PREPARE_GENOME {
} else if (gff) {
if (gff.endsWith('.gz')) {
ch_gff = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions).map { [ [:], it ] }
ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
} else {
ch_gff = Channel.value(file(gff, checkIfExists: true))
ch_gff = Channel.value(file(gff, checkIfExists: true)).map { [ [:], it ] }
}

ch_gtf = GFFREAD(ch_gff, []).gtf.map { it[1] }
Expand Down
⚡