Merge pull request #70 from sanger-tol/dev

Bug fix fasta for release

Author: gq1

.github/workflows/linting.yml

@@ -32,7 +32,7 @@ jobs:
       - uses: actions/setup-node@v3
 
       - name: Install Prettier
-        run: npm install -g prettier
+        run: npm install -g prettier@3.1.0
 
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}

CHANGELOG.md

@@ -3,6 +3,30 @@
 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).
 
+## [[1.1.1](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.1)] - Shang Zhou - [2024-02-02]
+
+### Enhancements & fixes
+
+- Bug fix when reference fasta file name end with .fa or .fa.gz
+
+### Parameters
+
+This release with the following initial parameters:
+
+| Old parameter | New parameter |
+| ------------- | ------------- |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
+
 ## [[1.1.0](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.0)] - Shang Tang - [2023-12-20]
 
 ### Enhancements & fixes

nextflow.config

@@ -215,7 +215,7 @@ manifest {
     description     = """Variant calling pipeline for PacBio data using DeepVariant"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.1.0'
+    version = '1.1.1'
     doi             = 'https://doi.org/10.5281/zenodo.7890527'
 }
 

subworkflows/local/input_filter_split.nf

@@ -54,7 +54,7 @@ workflow INPUT_FILTER_SPLIT {
      .map { meta, fasta -> [ fasta.baseName, fasta ] }
      .join ( 
         SAMTOOLS_FAIDX.out.fai
-         .map { mata, fai -> [ fai.baseName - '.fasta', fai ] } 
+         .map { mata, fai -> [ fai.baseName - ~/.fa\w*$/, fai ] } 
       )
      .set { fasta_fai }
 

workflows/variantcalling.nf

@@ -85,7 +85,7 @@ workflow VARIANTCALLING {
 
     ch_versions = Channel.empty()
     ch_fasta
-     .map { fasta -> [ [ 'id': fasta.baseName - '.fasta' - '.fa' ], fasta ] }
+     .map { fasta -> [ [ 'id': fasta.baseName -  ~/.fa\w*$/ ], fasta ] }
      .first()
      .set { ch_genome }