feat: Add linting of FASTQ with FQ/LINT

CHANGELOG.md

@@ -199,6 +199,7 @@ Akkatjåkkå is another glacier.
 ### 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
 

modules.json

@@ -181,6 +181,11 @@
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
+                    "fq/lint": {
+                        "branch": "master",
+                        "git_sha": "2c0260ed80daeca9c6dfa477a4daf04ff336dc37",
+                        "installed_by": ["modules"]
+                    },
                     "freebayes": {
                         "branch": "master",
                         "git_sha": "d04951ee68e3e8b875ebf5ddb7ba6e05233624c1",

nextflow_schema.json

@@ -118,7 +118,7 @@
                     "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"

workflows/sarek/main.nf

@@ -20,6 +20,9 @@ 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'
 include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_FQ_PAIR } from '../../modules/nf-core/spring/decompress'
 
+// Lint FASTQ with FQ/LINT
+include { FQ_LINT                                            } from '../../modules/nf-core/fq/lint/main'
+
 // Run FASTQC
 include { FASTQC                                            } from '../../modules/nf-core/fastqc'
 
@@ -178,6 +181,18 @@ workflow SAREK {
         // Or if we really want users to be able to do that
         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
         // `--skip_tools fastqc` to skip fastqc
         if (!(params.skip_tools && params.skip_tools.split(',').contains('fastqc'))) {