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feat: Add linting of FASTQ with FQ/LINT #1763

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feat: Add linting of FASTQ with FQ/LINT #1763

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8e174fa
feat: Add linting of FASTQ with FQ/LINT
adamrtalbot Dec 17, 2024
1f19f40
correct path import
adamrtalbot Dec 17, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added

- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev
- [1760](https://github.com/nf-core/sarek/pull/1760) - Add linting of FASTQ with FQ/LINT

### Changed

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5 changes: 5 additions & 0 deletions modules.json
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Expand Up @@ -174,6 +174,11 @@
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fq/lint": {
"branch": "master",
"git_sha": "2c0260ed80daeca9c6dfa477a4daf04ff336dc37",
"installed_by": ["modules"]
},
"freebayes": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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5 changes: 5 additions & 0 deletions modules/nf-core/fq/lint/environment.yml
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44 changes: 44 additions & 0 deletions modules/nf-core/fq/lint/main.nf
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43 changes: 43 additions & 0 deletions modules/nf-core/fq/lint/meta.yml
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63 changes: 63 additions & 0 deletions modules/nf-core/fq/lint/tests/main.nf.test
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25 changes: 25 additions & 0 deletions modules/nf-core/fq/lint/tests/main.nf.test.snap
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2 changes: 2 additions & 0 deletions modules/nf-core/fq/lint/tests/tags.yml
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -119,7 +119,7 @@
"fa_icon": "fas fa-forward",
"description": "Disable specified tools.",
"help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_tools baserecalibrator_report` is actually just not saving the reports.\n> **NB** `--skip_tools markduplicates_report` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.",
"pattern": "^((baserecalibrator|baserecalibrator_report|bcftools|dnascope_filter|documentation|fastqc|haplotypecaller_filter|haplotyper_filter|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)?,?)*(?<!,)$"
"pattern": "^((baserecalibrator|baserecalibrator_report|bcftools|dnascope_filter|documentation|fastqc|fq_lint|haplotypecaller_filter|haplotyper_filter|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)?,?)*(?<!,)$"
}
},
"fa_icon": "fas fa-user-cog"
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10 changes: 10 additions & 0 deletions workflows/sarek/main.nf
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Expand Up @@ -26,6 +26,9 @@ include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R1_FQ } from '../../module
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R2_FQ } from '../../modules/nf-core/spring/decompress/main'
include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_FQ_PAIR } from '../../modules/nf-core/spring/decompress/main'

// Lint FASTQ with FQ/LINT
include { FQ_LINT } from '../../modules/nf-core/fq_lint/main'

// Run FASTQC
include { FASTQC } from '../../modules/nf-core/fastqc/main'

Expand Down Expand Up @@ -199,10 +202,17 @@ workflow SAREK {
input_fastq = fastq_gz.mix(CONVERT_FASTQ_INPUT.out.reads).mix(one_fastq_gz_from_spring).mix(two_fastq_gz_from_spring)

// STEP 0: QC & TRIM
// `--skip_tools fq_lint` to skip linting with fq
// `--skip_tools fastqc` to skip fastqc
// Trim only with `--trim_fastq`
// Additional options to be set up

// Lint FASTQ with FQ/LINT
if (!params.skip_tools && params.skip_tools.split(',').contains('fq_lint')) {
FQ_LINT(input_fastq)
versions = versions.mix(FQ_LINT.out.versions)
}

// QC
if (!(params.skip_tools && params.skip_tools.split(',').contains('fastqc'))) {
FASTQC(input_fastq)
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