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Adding shortread deduplication feature with fastp #439

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Merged
jfy133 merged 14 commits into from
Feb 1, 2024
Merged

Adding shortread deduplication feature with fastp #439

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4add6c9
Merge pull request #388 from nf-core/dev
LilyAnderssonLee Oct 11, 2023
baede5b
Merge pull request #399 from nf-core/dev
jfy133 Oct 11, 2023
3d4eda2
Merge pull request #411 from nf-core/dev
jfy133 Oct 27, 2023
df4e001
Merge pull request #426 from nf-core/dev
jfy133 Jan 12, 2024
21e6af8
Merge pull request #435 from nf-core/dev
sofstam Jan 25, 2024
6c752a9
add fastp dedup
maxibor Jan 25, 2024
837a239
Merge branch 'fastp_dedup' into dev
maxibor Jan 25, 2024
2570c0f
update changelog
maxibor Jan 25, 2024
e6fdf57
Update CHANGELOG.md
maxibor Jan 26, 2024
6867467
Update nextflow_schema.json
maxibor Jan 26, 2024
47edb12
Update nextflow_schema.json
maxibor Jan 26, 2024
1fed057
Merge branch 'dev' into dedup
sofstam Jan 26, 2024
ea35f93
Prettier
sofstam Jan 26, 2024
7e3f119
Apply suggestions from code review
jfy133 Feb 1, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#439](https://github.com/nf-core/taxprofiler/pull/439) Read deduplication with fastp (added by @maxibor)

### `Fixed`

### `Dependencies`
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6 changes: 4 additions & 2 deletions conf/modules.config
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Expand Up @@ -57,7 +57,8 @@ process {
params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
// filtering options
"--length_required ${params.shortread_qc_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 ${params.shortread_complexityfilter_fastp_threshold}" : '',
params.shortread_qc_dedup ? "--dedup" : ""
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
Expand Down Expand Up @@ -93,7 +94,8 @@ process {
params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
// filtering options
"--length_required ${params.shortread_qc_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 ${params.shortread_complexityfilter_fastp_threshold}" : '',
params.shortread_qc_dedup ? "--dedup" : ""
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -71,6 +71,7 @@ params {
shortread_qc_adapter2 = null
shortread_qc_adapterlist = null
shortread_qc_minlength = 15
shortread_qc_dedup = false

perform_longread_qc = false
longread_qc_skipadaptertrim = false
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6 changes: 6 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -147,6 +147,12 @@
"description": "Specify the minimum length of reads to be retained",
"help_text": "Specifying a mimum read length filtering can speed up profiling by reducing the number of short unspecific reads that need to be match/aligned to the database.\n\n> Modifies tool parameter(s):\n> - removed from reads `--length_required`\n> - AdapterRemoval: `--minlength`"
},
"shortread_qc_dedup": {
"type": "boolean",
"fa_icon": "fas fa-toggle-on",
"description": "Perform deduplication of the input reads (fastp only)",
"help_text": "This enables the deduplication of processed reads during fastp adapter removal and/or merging. It removes identical reads that are likely artefacts from laboratory protocols (e.g. amplification), and provide no additional sequence information to the library.\n\nRemoving duplicates can increase runtime and increase accuracy of abundance calculations.\n\n> Modifies tool parameter(S):\n> fastp: ` --dedup`\n"
},
"perform_shortread_complexityfilter": {
"type": "boolean",
"fa_icon": "fas fa-toggle-on",
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