add fq lint

README.md

@@ -31,8 +31,8 @@
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
-2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+2. Validate fastq pairs ([`FQ`](https://github.com/stjude-rust-labs/fq))
 3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage

conf/modules.config

@@ -26,6 +26,22 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: FQ_LINT {
+        ext.args   = '--lint-mode log'
+        publishDir = [
+            [
+                path: { "${params.outdir}/fq/lint" },
+                mode: params.publish_dir_mode,
+                pattern: "*.log"
+            ],
+            [
+                path: { "${params.outdir}/fq/lint" },
+                mode: params.publish_dir_mode,
+                pattern: "*.txt"
+            ]
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

modules.json

@@ -10,6 +10,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "fq/lint": {
+                        "branch": "master",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",

workflows/seqinspector.nf

@@ -6,6 +6,7 @@
 
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample/main'
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
+include { FQ_LINT                       } from '../modules/nf-core/fq/lint/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -58,6 +59,14 @@ workflow SEQINSPECTOR {
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
+    //
+    // MODULE: Run FastQC
+    //
+    FQ_LINT (
+        ch_samplesheet
+    )
+    ch_versions = ch_versions.mix(FQ_LINT.out.versions)
+
     //
     // Collate and save software versions
     //