From d67543503b927f6af5bce9574ad8b428c53c0c46 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 7 May 2022 13:15:21 +0200 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Moritz E. Beber --- conf/modules.config | 2 +- docs/usage.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 0abff92..5d8398e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -55,7 +55,7 @@ process { params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "", // filtering options "--length_required ${params.shortread_clipmerge_minlength}", - params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : '' + (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : '' ].join(' ').trim() ext.prefix = { "${meta.id}_${meta.run_accession}" } publishDir = [ diff --git a/docs/usage.md b/docs/usage.md index 47ac952..54ffce0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -185,7 +185,7 @@ Complexity filtering is primarily a run-time optimisation step. It is not necess There are currently three options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/), [`prinseq++`](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus), and [`fastp`](https://github.com/OpenGene/fastp#low-complexity-filter). -The tools offer different algorithms and parameters for removing low complexity reads. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of both tools (see links above) to decide on optimal methods and parameters for your dataset. +The tools offer different algorithms and parameters for removing low complexity reads. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of the tools (see links above) to decide on optimal methods and parameters for your dataset. You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`. If running with `fastp`, complexity filtering happens inclusively within the earlier shortread preprocessing step. Therefore there will not be an independent pipeline step for complexity filtering, and no independent FASTQ file (i.e. `--save_complexityfiltered_reads` will be ignored) - your complexity filtered reads will also be in the `fastp/` folder in the same file(s) as the preprocessed read.