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Merged
jfy133 merged 3 commits into from
Mar 17, 2022
Merged

Add step size to lc_extrap docs #841

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307a621
Add step size to lc_extrap docs
jfy133 Mar 10, 2022
01a9cf7
Update CHANGELOG
jfy133 Mar 10, 2022
e4ba61b
Merge branch 'dev' into preseq-docs
jfy133 Mar 17, 2022
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -12,9 +12,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#828](https://github.com/nf-core/eager/issues/828) Improved error message if required metagenomic screening parameters not set correctly
- [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow
- [#845](https://github.com/nf-core/eager/issues/845) Updates parameter documention to specify `-s` preseq parameter also applies to lc_extrap
- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
- Fix PMDtools reference mask not being picked up by Nextflow, and it's use being evaluated against --snpcapture_bed rather than --pmdtools_reference_mask
- Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample

### `Dependencies`

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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -806,7 +806,7 @@
"default": 1000,
"description": "Specify the step size of Preseq.",
"fa_icon": "fas fa-shoe-prints",
"help_text": "Can be used to configure the step size of Preseq's `c_curve` method. Can be useful when only few and thus shallow sequencing results are used for extrapolation.\n\n> Modifies preseq c_curve parameter: `-s`"
"help_text": "Can be used to configure the step size of Preseq's `c_curve` and `lc_extrap` method. Can be useful when only few and thus shallow sequencing results are used for extrapolation.\n\n> Modifies preseq c_curve and lc_extrap parameter: `-s`"
},
"preseq_maxextrap": {
"type": "integer",
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