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Ensure pseudoaligner is set if pseudoalignment is not skipped #1124

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merged 13 commits into from
Nov 21, 2023
Merged

Ensure pseudoaligner is set if pseudoalignment is not skipped #1124

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7533e9f
Ensure pseudoaligner is set if pseudoalignment is not skipped
pinin4fjords Nov 20, 2023
10d8086
Update changelog
pinin4fjords Nov 20, 2023
279fd12
[skip ci] bump version in config
pinin4fjords Nov 20, 2023
8ed06f3
Move release to minor version, include tximport PR
pinin4fjords Nov 20, 2023
8615a86
[skip ci] Back to patch release
pinin4fjords Nov 20, 2023
0a675cf
Fix error message
pinin4fjords Nov 20, 2023
05c4918
Merge branch 'dev' into ensure_notnull_pseudo
pinin4fjords Nov 20, 2023
e1a5cca
[automated] Fix linting with Prettier
nf-core-bot Nov 20, 2023
0f6fec6
Merge branch 'ensure_notnull_pseudo' of github.com:nf-core/rnaseq int…
pinin4fjords Nov 20, 2023
89666a4
Add credits
pinin4fjords Nov 20, 2023
065c63a
Merge branch 'dev' into ensure_notnull_pseudo
pinin4fjords Nov 20, 2023
36c4204
[skipci] Update CHANGELOG.md
drpatelh Nov 21, 2023
cfd9270
Always check --skip_pseudo_alignment and --pseudo_aligner are set
drpatelh Nov 21, 2023
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8 changes: 7 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,11 +3,17 @@
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).

## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-20

### Enhancements & fixes

- [PR #1124](https://github.com/nf-core/rnaseq/pull/1124) - Ensure pseudoaligner is set if pseudoalignment is not skipped

## [[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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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -58,7 +58,7 @@ params {

// Alignment
aligner = 'star_salmon'
pseudo_aligner = null
pseudo_aligner = 'salmon'
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seq_center = null
bam_csi_index = false
star_ignore_sjdbgtf = false
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8 changes: 7 additions & 1 deletion workflows/rnaseq.nf
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Expand Up @@ -37,7 +37,13 @@ if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list)
def prepareToolIndices = []
if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' }
if (!params.skip_alignment) { prepareToolIndices << params.aligner }
if (!params.skip_pseudo_alignment && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner }
if (!params.skip_pseudo_alignment) {
if(params.pseudo_aligner) {
prepareToolIndices << params.pseudo_aligner
} else {
exit 1, "--skip_pseudo_alignment not set, but --pseudo_aligner not set"
}
}

// Determine whether to filter the GTF or not
def filterGtf =
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