From 3153907490db3cfd979af89b8ee11d3c4fd8dfb4 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 24 Dec 2024 11:42:15 +0100 Subject: [PATCH] Fix GFFREAD when gff file provided by user (add empty map to channel) --- CHANGELOG.md | 1 + subworkflows/local/prepare_genome.nf | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 98c7d5588..08e5578ac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index b053c2193..0e3144778 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -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] }