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bugfix/update-fasta-help #494

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merged 4 commits into from
Dec 23, 2024
Merged

bugfix/update-fasta-help #494

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02a2724
Updata help text for --fasta parameter
kopichris Dec 17, 2024
1e7e716
Update CHANGELOG.md
kopichris Dec 17, 2024
ba88b1e
Merge branch 'dev' into bugfix/update-fasta-help
atrigila Dec 18, 2024
d768833
Undo change to default value for save_merged param
kopichris Dec 23, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#481]](https://github.com/nf-core/smrnaseq/pull/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.
- [[#482]](https://github.com/nf-core/smrnaseq/pull/482) - Update documentation regarding MirgeneDB input files.
- [[#486]](https://github.com/nf-core/smrnaseq/pull/486) - Replace `CSVTK_JOIN` to improve processing in large amount of files.
- [[#494]](https://github.com/nf-core/smrnaseq/pull/494) - Update [help text](https://github.com/nf-core/smrnaseq/issues/491) for `--fasta` parameter
- [[#493]](https://github.com/nf-core/smrnaseq/pull/493) - Fix [[#488]](https://github.com/nf-core/smrnaseq/issues/488) - Fix runtime error that can occur when params.genome is set.

## v2.4.0 - 2024-10-14 - Navy Iron Boxer
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5 changes: 2 additions & 3 deletions nextflow_schema.json
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Expand Up @@ -133,7 +133,7 @@
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"help_text": "FASTA file used for genome quantification and identification of novel miRNAs. If you don't have a Bowtie1 index available, this will be generated for you automatically. Combine with `--save_reference` to save Bowtie1 index for future runs.",
"fa_icon": "far fa-file-code"
},
"mirna_gtf": {
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},
"save_merged": {
"type": "boolean",
"description": "Save merged reads.",
"default": false
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Why is the default false removed here?

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I'll update the PR. Not sure why this got removed. Thanks for catching this.

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Updated the PR in d768833. Thanks again!

"description": "Save merged reads."
},
"phred_offset": {
"type": "integer",
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