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Adjust fastp parameters #203

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Merged
skrakau merged 5 commits into from
May 27, 2021
Merged

Adjust fastp parameters #203

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73bb74d
Renamed param --mean_quality to --fastp_qualified_quality and adjuste…
skrakau May 27, 2021
e0f17e5
Renamed param --trimming_quality to --fastp_cut_mean_quality and adju…
skrakau May 27, 2021
8d94692
Replaced deprecated fastp params --cut_by_quality5/3 by --cut_front/tail
skrakau May 27, 2021
2b51c46
Adjust desscription of fast param --save_trimmed_fail
skrakau May 27, 2021
255653b
Update CHANGELOG
skrakau May 27, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#193](https://github.com/nf-core/mag/pull/193) - Compress CAT output files [#180](https://github.com/nf-core/mag/issues/180)
- [#198](https://github.com/nf-core/mag/pull/198) - Requires nextflow version `>= 21.04.0`
- [#200](https://github.com/nf-core/mag/pull/200) - Small changes in GitHub Actions tests
- [#203](https://github.com/nf-core/mag/pull/203) - Renamed `fastp` params and improved description in documentation: `--mean_quality` -> `--fastp_qualified_quality`, `--trimming_quality` -> `--fastp_cut_mean_quality`

### `Fixed`

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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -23,8 +23,8 @@ params {
publish_files = ['html':'']
publish_dir = "QC_shortreads/fastqc"
}
'fastp' { // TODO check parameter: -q vs -e?
args = "-q ${params.mean_quality} --cut_by_quality5 --cut_by_quality3 --cut_mean_quality ${params.trimming_quality}"
'fastp' {
args = "-q ${params.fastp_qualified_quality} --cut_front --cut_tail --cut_mean_quality ${params.fastp_cut_mean_quality}"
publish_files = ['html':'', 'json':'']
publish_by_id = true
publish_dir = "QC_shortreads/fastp"
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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -14,8 +14,8 @@ params {

// short read preprocessing options
save_trimmed_fail = false
mean_quality = 15
trimming_quality = 15
fastp_qualified_quality = 15
fastp_cut_mean_quality = 15
keep_phix = false
// phix_reference = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
phix_reference = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
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12 changes: 7 additions & 5 deletions nextflow_schema.json
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Expand Up @@ -300,18 +300,20 @@
"save_trimmed_fail": {
"type": "boolean",
"fa_icon": "fas fa-save",
"description": "Save the trimmed FastQ files in the results directory.",
"description": "Save the by fastp trimmed FastQ files in the results directory.",
"help_text": "By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete."
},
"mean_quality": {
"fastp_qualified_quality": {
"type": "integer",
"default": 15,
"description": "Mean qualified quality value for keeping read."
"description": "Minimum phred quality value of a base to be qualified.",
"help": "Reads with more than 40% of unqualified bases will be discarded."
},
"trimming_quality": {
"fastp_cut_mean_quality": {
"type": "integer",
"default": 15,
"description": "Trimming quality value for the sliding window."
"description": "The mean quality requirement used for per read sliding window cutting by fastp.",
"help": "Used in combination with the fastp options '--cut_front' and '--cut_tail'. If the mean quality within a window (of size 4) is below `--fastp_cut_mean_quality`, the bases are dropped and the sliding window is moved further, otherwise it stops."
},
"host_genome": {
"type": "string",
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