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Review suggestions on v2.3.0 #669

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Jan 22, 2025
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Review suggestions on v2.3.0 #669

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9864840
Annick's review suggestions
ramprasadn Jan 22, 2025
6dfb6f1
prettier
ramprasadn Jan 22, 2025
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608)
- An option to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
- An option `extract_alignments` to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
- Fastp and ngsbits output files as input of MultiQC [#647](https://github.com/nf-core/raredisease/pull/647/).
- Haplocheck output file as input of MultiQC [#662](https://github.com/nf-core/raredisease/pull/662)

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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -185,7 +185,7 @@ The mandatory and optional parameters for each category are tabulated below.
<sup>4</sup>fasta_fai, bwa, bwamem2 and bwameme, if not provided by the user, will be generated by the pipeline when necessary.<br />
<sup>5</sup>Used only by Sentieon.<br />
<sup>6</sup>Default value is 40. Used only by fastp.<br />
<sup>7</sup>Used to limit your analysis to specific contigs. Can be used to remove alignments to unplaced contigs to minimize potential errors. This parameter should be used in conjuction with `extract_alignments` parameter.<br />
<sup>7</sup>Used to limit your analysis to specific contigs. Can be used to remove alignments to unplaced contigs to minimize potential errors. This parameter should be used in conjunction with the `extract_alignments` parameter.<br />

##### 2. QC stats from the alignment files

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