Merge pull request #232 from jonasscheid/prepare-release

Prepare release

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.3.0 - Oesterberg - 2024-02-14
+## v2.3.0 - Oesterberg - 2024-02-20
 
 ### `Changed`
 

assets/schema_input.json

@@ -45,7 +45,7 @@
             "filename": {
                 "type": "string",
                 "pattern": "^\\S+\\.(vcf|vcf.gz|tsv|fasta|fa)$",
-                "errorMessage": "Variants/proteins/peptides for sample must be provided and have one of the following extensions: '.vcf', '.vcf.gz', '.tsv', '.fasta', '.fa'"
+                "errorMessage": "Variants/proteins/peptides of a sample must be provided and have one of the following extensions: '.vcf', '.vcf.gz', '.tsv', '.fasta', '.fa'"
             }
         },
         "required": ["sample", "alleles", "mhc_class", "filename"]

bin/check_requested_models.py

@@ -74,12 +74,7 @@ def __main__():
         }
 
     # get the alleles
-    if args.alleles.startswith("http"):
-        alleles = [Allele(a) for a in urllib.request.urlopen(args.alleles).read().decode("utf-8").splitlines()]
-    elif args.alleles.endswith(".txt"):
-        alleles = [Allele(a) for a in open(args.alleles).read().splitlines()]
-    else:
-        alleles = [Allele(a) for a in args.alleles.split(";")]
+    alleles = [Allele(a) for a in args.alleles.split(";")]
 
     peptide_lengths = []
     if args.peptides:

docs/usage.md

@@ -23,8 +23,7 @@ The pipeline currently accepts three different types of input that are genomic v
 The supported file formats for genomic variants are `.vcf`, `.vcf.gz` and `tsv`.
 
 > [!IMPORTANT]
-> Please note that genomic variants have to be annotated. Currently, we support variants that have been annotated using [SnpEff](http://pcingola.> github.io/SnpEff/).
-> Support for [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html) will be available with one of the upcoming versions.
+> Please note that genomic variants have to be annotated. Currently, we support variants that have been annotated using [SnpEff](http://pcingola.> github.io/SnpEff/) and [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html).
 
 `tsv` files with genomic variants have to provide the following columns:
 
@@ -36,7 +35,7 @@ chr1 12954870 12954870 C T . 0 NORMAL:414,TUMOR:8 . missense_variant 0.5 transcr
 
 ```
 
-For genomic variants, reference information from `Ensembl BioMart` is used. The default database version is the most recent `GRCh37` version. If you want to do the predictions based on `GRCh38` as the reference genome, please specify `--genome_reference grch37` in your pipeline call.
+For genomic variants, reference information from `Ensembl BioMart` is used. The default database version is the most recent `GRCh37` version. If you want to do the predictions based on `GRCh38` as the reference genome, please specify `--genome_reference grch38` in your pipeline call.
 
 You can also specify valid `Ensembl BioMart` archive version urls as `--genome_reference` value, e.g. [the archive version of December 2021](http://dec2021.archive.ensembl.org/).
 

lib/WorkflowEpitopeprediction.groovy

@@ -54,7 +54,6 @@ class WorkflowEpitopeprediction {
         // Uncomment function in methodsDescriptionText to render in MultiQC report
         def citation_text = [
                 "Tools used in the workflow included:",
-                "FastQC (Andrews 2010),",
                 "MultiQC (Ewels et al. 2016)",
                 "."
             ].join(' ').trim()
@@ -68,7 +67,6 @@ class WorkflowEpitopeprediction {
         // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
         // Uncomment function in methodsDescriptionText to render in MultiQC report
         def reference_text = [
-                "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
                 "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
             ].join(' ').trim()