From 91c51f48ea14f97e889a193fc28e21c162b03227 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 23 Aug 2021 21:38:07 +0200 Subject: [PATCH] Update best practise defults and bam trimming defaults --- CHANGELOG.md | 2 ++ nextflow.config | 14 +++++++------- nextflow_schema.json | 12 ++++++------ 3 files changed, 15 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c531715b..3a72f5728 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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` diff --git a/nextflow.config b/nextflow.config index 0a405044d..c7a8d8703 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 @@ -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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 4ae9d6891..d25b1ba30 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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`" @@ -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" @@ -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`"