Address review comments

README.md

@@ -33,7 +33,10 @@
   <img alt="Fallback image description" src="docs/images/nfcore-seqinspector-logo-hex-light.png">
 </picture>
 
-**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
+**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.
+It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.
+The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
+If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
 
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 

docs/output.md

@@ -78,7 +78,7 @@ To use FastQ Screen, this pipeline requires a `.csv` detailing:
 
 - the working name of the reference
 - the name of the aligner used to generate its index (which is also the aligner and index used by the tool)
-- the file basename of the reference and its index (e.g. the reference `genoma.fa` and its index `genome.bt2` have the basename `genome`)
+- the file basename of the reference and its index (e.g. the reference `genome.fa` and its index `genome.bt2` have the basename `genome`)
 - the path to a dir where the reference and index files both reside.
 
 See `assets/example_fastq_screen_references.csv` for example.

modules/local/rundirparser/resources/usr/bin/parse_illumina.py

@@ -1,5 +1,8 @@
 #!/usr/bin/env python3
 
+# Author: @matrulda
+# Licence: MIT
+
 import os
 import yaml
 import sys
@@ -18,8 +21,10 @@ def read_run_parameters(directory):
         with open(alt_2) as f:
             return xmltodict.parse(f.read())
     else:
-        raise Exception("Could not find Illumina [Rr]unParameters.xml. "
-                        "Please provide RunParameters.xml or skip module.")
+        raise Exception(
+            "Could not find Illumina [Rr]unParameters.xml. "
+            "Please provide RunParameters.xml or skip module."
+        )
 
 
 def find(d, tag):
@@ -71,12 +76,11 @@ def construct_multiqc_yaml(directory):
         "description": "Sequencing metadata gathered from the run directory",
         "plot_type": "table",
         "pconfig": {
-            "id": 'mqc_seq_metadata',
-            "title": 'Run directory Metadata',
+            "id": "mqc_seq_metadata",
+            "title": "Run directory Metadata",
             "col1_header": "Metadata",
-            },
+        },
         "data": data,
-
     }
 
     return metadata

nextflow.config

@@ -252,12 +252,150 @@ manifest {
     name            = 'nf-core/seqinspector'
     contributors    = [
         [
-            name: 'National Genomics Infrastructure',
-            affiliation: '',
-            email: '',
-            github: 'https://github.com/NationalGenomicsInfrastructure/',
-            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            name: 'Adrien Coulier',
+            affiliation: 'Pixelgen Technologies',
+            github: 'Aratz',
+            contribution: ['author']
+        ],
+        [
+            name: 'Alfred Kedhammar',
+            affiliation: 'Clinical Genomics',
+            github: 'kedhammar',
+            contribution: ['author']
+        ],
+        [
+            name: 'Agrima Bhatt',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'agrima2010',
+            orcid: '0009-0004-5536-7210'
+            contribution: ['author']
+        ],
+        [
+            name: 'Maxime U Garcia',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'maxulysse',
+            contribution: ['maintainer'],
+            orcid: '0000-0003-2827-9261'
+        ],
+        [
+            name: 'Natalia Garcia Garcia',
+            github: 'nggvs',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Franziska Bonath',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'FranBonath',
+            contribution: ['author']
+        ],
+        [
+            name: 'Pontus Höjer',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'pontushojer',
+            contribution: ['contributor'],
+            orcid: '0000-0001-8010-4755'
+        ],
+        [
+            name: 'Edmund Miller',
+            affiliation: 'Seqera',
+            github: 'edmundmiller',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Mahesh Binzer-Panchal',
+            affiliation: 'National Bioinformatics Infrastructure Sweden',
+            github: 'mahesh-panchal',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Ramprasad Neethiraj',
+            affiliation: 'Clinical Genomics',
+            github: 'ramprasadn',
+            contribution: ['author']
+        ],
+        [
+            name: 'Matilda Åslin',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'matrulda',
+            contribution: ['author']
+        ],
+        [
+            name: 'Patricie Skaláková',
+            affiliation: 'Masaryk University',
+            github: 'Patricie34',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Eliott Bosshard',
+            affiliation: 'Clinical Genomics',
+            github: 'EliottBo',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Karthik Nair',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'KarNair',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Matthias Zepper',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'MatthiasZepper',
+            contribution: ['author']
+        ],
+        [
+            name: 'Nelly Nyawira Nkonge',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'nkongenelly',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Beatriz Vinhas',
+            affiliation: 'Clinical Genomics',
+            github: 'beatrizsavinhas',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Júlia Mir Pedrol',
+            affiliation: 'Center For Genomics Regulation',
+            github: 'mirpedrol',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Cristina Tuñí i Domínguez',
+            affiliation: 'Flowmics',
+            github: 'ctuni',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Johannes Alneberg',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'alneberg',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Annick Renevey',
+            affiliation: 'Clinical Genomics',
+            github: 'rannick',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Adam Talbot',
+            affiliation: 'Seqera',
+            github: 'adamrtalbot',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Jonas Kjellin',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'kjellinjonas',
+            contribution: ['contributor']
+        ],
+        [
+            name: 'Tori Griffin',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'torigiffin',
+            contribution: ['contributor']
         ],
     ]
     homePage        = 'https://github.com/nf-core/seqinspector'