Add long reads

CHANGELOG.md

@@ -21,8 +21,10 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
+- [#109](https://github.com/nf-core/seqinspector/pull/109) Adds ToulligQC module for long read QC
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
 
+
 ### `Fixed`
 
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.

CITATIONS.md

@@ -28,6 +28,8 @@
 
 - [Seqtk](https://github.com/lh3/seqtk)
 
+- [ToulligQC](https://github.com/GenomiqueENS/toulligQ)
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

assets/multiqc_config.yml

@@ -2,6 +2,7 @@ report_comment: >
   This report has been generated by the <a href="https://github.com/nf-core/seqinspector/tree/dev" target="_blank">nf-core/seqinspector</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
+  If ToulligQC was used, a separate report is available in the results folder.
 report_section_order:
   "nf-core-seqinspector-methods-description":
     order: -1000

conf/modules.config

@@ -35,6 +35,15 @@ process {
         ]
     }
 
+    withName: 'TOULLIGQC' {
+        ext.args = ''
+        publishDir = [
+            path: { "${params.outdir}/toulligqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

docs/output.md

@@ -80,6 +80,17 @@ The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is
 
 [SeqFu](https://telatin.github.io/seqfu2/) is general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
 
+### ToulligQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `toulligqc/`
+  - `*.data`: ToulligQC output text file containing log information and all analysis results
+  - `*.html`: ToulligQC html report file
+
+[ToulligQC](https://github.com/GenomiqueENS/toulligQC) is dedicated to the QC analyses of Oxford Nanopore runs. This software is written in Python and developped by the GenomiqueENS core facility of the Institute of Biology of the Ecole Normale Superieure (IBENS).
+
 ### MultiQC
 
 nf-core/seqinspector will generate the following MultiQC reports:

modules.json

@@ -40,6 +40,11 @@
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
+                    },
+                    "toulligqc": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
                     }
                 }
             },