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Fix pipeline failure when transcript_fasta not provided and skip_gtf_filter is set to TRUE #1126

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merged 5 commits into from
Nov 20, 2023
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Fix pipeline failure when transcript_fasta not provided and skip_gtf_filter is set to TRUE #1126

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249c2a9
fix: remove GTF_FILTER.out.versions
rhr-cosyne Nov 20, 2023
5c50f7d
docs: update CHANGELOG
RHReynolds Nov 20, 2023
1398f5c
docs: move update to dev
RHReynolds Nov 20, 2023
317e2e0
Fix CHANGELOG.md
pinin4fjords Nov 20, 2023
5e42930
[automated] Fix linting with Prettier
nf-core-bot Nov 20, 2023
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9 changes: 8 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,11 +3,18 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## dev

### Enhancements and fixes

- [PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true
- [#1125](https://github.com/nf-core/rnaseq/issues/1125) - Pipeline fails if transcript_fasta not provided and skip_gtf_filter = true

## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17

### Enhancements and fixes

- [[PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix
- [PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix

## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17

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7 changes: 3 additions & 4 deletions subworkflows/local/prepare_genome/main.nf
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Expand Up @@ -47,7 +47,7 @@ workflow PREPARE_GENOME {
rsem_index // directory: /path/to/rsem/index/
salmon_index // directory: /path/to/salmon/index/
kallisto_index // directory: /path/to/kallisto/index/
hisat2_index // directory: /path/to/hisat2/index/
hisat2_index // directory: /path/to/hisat2/index/
bbsplit_index // directory: /path/to/rsem/index/
gencode // boolean: whether the genome is from GENCODE
is_aws_igenome // boolean: whether the genome files are from AWS iGenomes
Expand Down Expand Up @@ -139,14 +139,13 @@ workflow PREPARE_GENOME {
} else {
ch_transcript_fasta = Channel.value(file(transcript_fasta))
}
if (gencode) {
if (gencode) {
PREPROCESS_TRANSCRIPTS_FASTA_GENCODE ( ch_transcript_fasta )
ch_transcript_fasta = PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.fasta
ch_versions = ch_versions.mix(PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.versions)
}
} else {
ch_transcript_fasta = MAKE_TRANSCRIPTS_FASTA ( ch_fasta, ch_gtf ).transcript_fasta
ch_versions = ch_versions.mix(GTF_FILTER.out.versions)
ch_versions = ch_versions.mix(MAKE_TRANSCRIPTS_FASTA.out.versions)
}

Expand Down Expand Up @@ -268,7 +267,7 @@ workflow PREPARE_GENOME {
ch_versions = ch_versions.mix(SALMON_INDEX.out.versions)
}
}

//
// Uncompress Kallisto index or generate from scratch if required
//
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