Adds fq/lint for early validation of FASTQs

Validation of FASTQS early prevents running the pipeline on invalid FASTQ files which will make the pipeline more efficient at achieving it's ultimate objective of checking FASTQ validity.

It adds 3 more parameters:
 - `--skip_linting` which enables the linting of FASTQs
 - `--fq_lint_args` which is a string of arguments to pass to the linting tool
 - `--continue_with_lint_fail` which is a boolean to determine whether to continue if the linting fails

Between these three options the user has a high degree of control over how the pipeline lints which should handle most use cases.

Closes #31

Author: adamrtalbot

CHANGELOG.md

@@ -17,6 +17,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
+- [#67](https://github.com/nf-core/seqinspector/pull/67) Add FASTQ linting for early validation
 
 ### `Fixed`
 

CITATIONS.md

@@ -10,6 +10,8 @@
 
 ## Pipeline tools
 
+- [FQ](https://github.com/stjude-rust-labs/fq)
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

README.md

@@ -31,9 +31,10 @@
      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. Lint FASTQs with ([`fq`](https://github.com/stjude-rust-labs/fq))
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
-2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+1. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

conf/modules.config

@@ -18,6 +18,15 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    withName: 'FQ_LINT' {
+        ext.args      = { params.fq_lint_args }
+        errorStrategy = {
+                            task.exitStatus in ((130..145) + 104) ? 'retry'  :
+                            params.continue_with_lint_fail        ? 'ignore' :
+                            'finish'
+                        }
+    }
+
     withName: SEQTK_SAMPLE {
         ext.args = '-s100'
     }

modules.json

@@ -8,38 +8,59 @@
                     "bowtie2/build": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
+                    "fq/lint": {
+                        "branch": "master",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -48,20 +69,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}