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add fastp args and add changelog #12

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May 24, 2024
Merged

add fastp args and add changelog #12

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45593bf
add fastp args and add changelog
May 24, 2024
600a914
Merge remote-tracking branch 'origin/master' into develop
May 24, 2024
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25 changes: 25 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -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
8 changes: 4 additions & 4 deletions modules/01_fastp.nf
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Expand Up @@ -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)
Expand All @@ -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 ${fastq1.baseName}.trimmed.fq.gz \
Expand All @@ -41,7 +41,7 @@ process FASTP_SINGLE {
publishDir "${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)
Expand All @@ -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 \
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2 changes: 2 additions & 0 deletions nextflow.config
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Expand Up @@ -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 {
Expand Down Expand Up @@ -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
Expand Down
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