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Update best practise defults and bam trimming defaults #784

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Merged
jfy133 merged 1 commit into from
Aug 24, 2021
Merged

Update best practise defults and bam trimming defaults #784

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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#771](https://github.com/nf-core/eager/issues/771) Remove legacy code
- Improved output documentation for MultiQC general stats table (thanks to @KathrinNaegele and @esalmela)
- Improved output documentation for BowTie2 (thanks to @isinaltinkaya)
- [#612](https://github.com/nf-core/eager/issues/612) Updated BAM trimming defaults to 0 to ensure no unwanted trimming when mixing half-UDG with no-UDG (thanks to @scarlhoff)
- [#722](https://github.com/nf-core/eager/issues/722) Updated BWA mapping mapping parameters to latest recommendations - primarily alnn back to 0.01 and aln0 to 2 as per Oliva et al. 2021 (10.1093/bib/bbab076)

### `Dependencies`

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14 changes: 7 additions & 7 deletions nextflow.config
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Expand Up @@ -83,10 +83,10 @@ params {

//Mapping algorithm
mapper = 'bwaaln'
bwaalnn = 0.04
bwaalnn = 0.01 // From Oliva et al. 2021 (10.1093/bib/bbab076)
bwaalnk = 2
bwaalnl = 1024 // From Schubert et al. 2012 (10.1186/1471-2164-13-178)
bwaalno = 1 // leave at bwa default for now
bwaalnl = 1024 // From Oliva et al. 2021 (10.1093/bib/bbab076)
bwaalno = 2 // From Oliva et al. 2021 (10.1093/bib/bbab076)
circularextension = 500
circulartarget = 'MT'
circularfilter = false
Expand Down Expand Up @@ -144,10 +144,10 @@ params {

//bamUtils trimbam settings
run_trim_bam = false
bamutils_clip_half_udg_left = 1
bamutils_clip_half_udg_right = 1
bamutils_clip_none_udg_left = 1
bamutils_clip_none_udg_right = 1
bamutils_clip_half_udg_left = 0
bamutils_clip_half_udg_right = 0
bamutils_clip_none_udg_left = 0
bamutils_clip_none_udg_right = 0
bamutils_softclip = false

//Genotyping options
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12 changes: 6 additions & 6 deletions nextflow_schema.json
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Expand Up @@ -577,7 +577,7 @@
},
"bwaalnn": {
"type": "number",
"default": 0.04,
"default": 0.01,
"description": "Specify the -n parameter for BWA aln, i.e. amount of allowed mismatches in the alignment.",
"fa_icon": "fas fa-sort-numeric-down",
"help_text": "Configures the `bwa aln -n` parameter, defining how many mismatches are allowed in a read. By default set to `0.04` (following recommendations of [Schubert et al. (2012 _BMC Genomics_)](https://doi.org/10.1186/1471-2164-13-178)), if you're uncertain what to set check out [this](https://apeltzer.shinyapps.io/bwa-mismatches/) Shiny App for more information on how to set this parameter efficiently.\n\n> Modifies bwa aln parameter: `-n`"
Expand All @@ -598,7 +598,7 @@
},
"bwaalno": {
"type": "integer",
"default": 1,
"default": 2,
"fa_icon": "fas fa-people-arrows",
"description": "Specify the -o parameter for BWA aln i.e. the number of gaps allowed.",
"help_text": "Configures the number of gaps used in `bwa aln`. Default is set to `bwa` default.\n\n> Modifies BWA aln parameter: `-o`\n"
Expand Down Expand Up @@ -966,28 +966,28 @@
},
"bamutils_clip_half_udg_left": {
"type": "integer",
"default": 1,
"default": 0,
"fa_icon": "fas fa-ruler-combined",
"description": "Specify the number of bases to clip off reads from 'left' end of read for half-UDG libraries.",
"help_text": "Default set to `1` and clips off one base of the left or right side of reads from libraries whose UDG treatment is set to `half`. Note that reverse reads will automatically be clipped off at the reverse side with this (automatically reverses left and right for the reverse read).\n\n> Modifies bamUtil's trimBam parameter: `-L -R`"
},
"bamutils_clip_half_udg_right": {
"type": "integer",
"default": 1,
"default": 0,
"fa_icon": "fas fa-ruler",
"description": "Specify the number of bases to clip off reads from 'right' end of read for half-UDG libraries.",
"help_text": "Default set to `1` and clips off one base of the left or right side of reads from libraries whose UDG treatment is set to `half`. Note that reverse reads will automatically be clipped off at the reverse side with this (automatically reverses left and right for the reverse read).\n\n> Modifies bamUtil's trimBam parameter: `-L -R`"
},
"bamutils_clip_none_udg_left": {
"type": "integer",
"default": 1,
"default": 0,
"fa_icon": "fas fa-ruler-combined",
"description": "Specify the number of bases to clip off reads from 'left' end of read for non-UDG libraries.",
"help_text": "Default set to `1` and clips off one base of the left or right side of reads from libraries whose UDG treatment is set to `none`. Note that reverse reads will automatically be clipped off at the reverse side with this (automatically reverses left and right for the reverse read).\n\n> Modifies bamUtil's trimBam parameter: `-L -R`"
},
"bamutils_clip_none_udg_right": {
"type": "integer",
"default": 1,
"default": 0,
"fa_icon": "fas fa-ruler",
"description": "Specify the number of bases to clip off reads from 'right' end of read for non-UDG libraries.",
"help_text": "Default set to `1` and clips off one base of the left or right side of reads from libraries whose UDG treatment is set to `none`. Note that reverse reads will automatically be clipped off at the reverse side with this (automatically reverses left and right for the reverse read).\n\n> Modifies bamUtil's trimBam parameter: `-L -R`"
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