diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..a65facf --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,25 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [1.9.0] - 2024-05-24 + +### Added + +- Add the parameter `--fastp_args` to provide any arbitrary parameters to fastp + +### Changed + +- Fastp version is upgraded from 0.20.1 to o.23.4 + + +To be completed... + + + + +[unreleased]: https://github.com/olivierlacan/keep-a-changelog/compare/v1.9.0...HEAD +[1.9.0]: https://github.com/olivierlacan/keep-a-changelog/compare/v1.8.1...v1.9.0 diff --git a/modules/01_fastp.nf b/modules/01_fastp.nf index a972813..5d57e5d 100644 --- a/modules/01_fastp.nf +++ b/modules/01_fastp.nf @@ -6,7 +6,7 @@ process FASTP_PAIRED { publishDir "${params.output}", mode: "copy", pattern: "*fastp_stats*" publishDir "${params.output}/${name}/", mode: "copy", pattern: "software_versions.*" - conda (params.enable_conda ? "bioconda::fastp=0.20.1" : null) + conda (params.enable_conda ? "bioconda::fastp=0.23.4" : null) input: tuple val(name), file(fastq1), file(fastq2) @@ -20,7 +20,7 @@ process FASTP_PAIRED { """ # --input_files needs to be forced, otherwise it is inherited from profile in tests - fastp \ + fastp ${params.fastp_args} \ --in1 ${fastq1} \ --in2 ${fastq2} \ --out1 ${fastq1.baseName}.trimmed.fq.gz \ @@ -41,7 +41,7 @@ process FASTP_SINGLE { publishDir "${params.output}", mode: "copy", pattern: "*fastp_stats*" publishDir "${params.output}/${name}/", mode: "copy", pattern: "software_versions.*" - conda (params.enable_conda ? "bioconda::fastp=0.20.1" : null) + conda (params.enable_conda ? "bioconda::fastp=0.23.4" : null) input: tuple val(name), file(fastq1) @@ -54,7 +54,7 @@ process FASTP_SINGLE { """ # --input_files needs to be forced, otherwise it is inherited from profile in tests - fastp \ + fastp ${params.fastp_args} \ --in1 ${fastq1} \ --out1 ${fastq1.baseName}.trimmed.fq.gz \ --json ${name}.fastp_stats.json \ diff --git a/nextflow.config b/nextflow.config index d909fe8..819a5b8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -18,6 +18,7 @@ params.inception = false params.skip_trimming = false params.star_two_pass_mode = false params.additional_args = "" +params.fastp_args = "" profiles { conda { @@ -88,6 +89,7 @@ Optional input: * skip_trimming: skips the read trimming step * star_two_pass_mode: activates STAR two-pass mode, increasing sensitivity of novel junction discovery, recommended for RNA variant calling (default: false) * additional_args: additional alignment arguments, only effective in BWA mem, BWA mem 2 and STAR (default: none) + * fastp_args: additional fastp arguments (default: none) Output: * A BAM file \${name}.bam and its index