Merge pull request #285 from nf-core/dev

Dev -> Master for 2.4 release

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/vira
     - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/viralrecon _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/ci.yml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
   parameters:
     name: Test workflow parameters
@@ -74,7 +74,7 @@ jobs:
 
       - name: Run pipeline with various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
 
   test_sispa:
     name: Test SISPA workflow
@@ -96,7 +96,7 @@ jobs:
 
       - name: Run pipeline with minimal SISPA data and various options
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }} --outdir ./results
 
   test_nanopore:
     name: Test Nanopore workflow
@@ -110,6 +110,7 @@ jobs:
           - "--min_barcode_reads 10000"
           - "--min_guppyplex_reads 10000"
           - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false"
+          - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model r941_min_high_g360"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -121,4 +122,4 @@ jobs:
 
       - name: Run pipeline with minimal Nanopore data and various options
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }} --outdir ./results

.nf-core.yml

@@ -5,6 +5,7 @@ lint:
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
     - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
     - .github/workflows/branch.yml
     - .github/workflows/linting_comment.yml
     - .github/workflows/linting.yml

CHANGELOG.md

@@ -3,6 +3,26 @@
 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).
 
+## [[2.4](https://github.com/nf-core/viralrecon/releases/tag/2.4)] - 2022-02-22
+
+### Enhancements & fixes
+
+* [nf-core/tools#1415](https://github.com/nf-core/tools/issues/1415) - Make `--outdir` a mandatory parameter
+* [[#281](https://github.com/nf-core/viralrecon/issues/281)] - Nanopore medaka processing fails with error if model name, not model file, provided
+* [[#286](https://github.com/nf-core/viralrecon/issues/286)] - IVAR_VARIANTS silently failing when FAI index is missing
+
+### Parameters
+
+| Old parameter                 | New parameter                         |
+|-------------------------------|---------------------------------------|
+|                               | `--publish_dir_mode`                  |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present.
+>
+> **NB:** Parameter has been **added** if just the new parameter information is present.
+>
+> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
 ## [[2.3.1](https://github.com/nf-core/viralrecon/releases/tag/2.3.1)] - 2022-02-15
 
 ### Enhancements & fixes

README.md

@@ -87,7 +87,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run nf-core/viralrecon -profile test,YOURPROFILE
+    nextflow run nf-core/viralrecon -profile test,YOURPROFILE --outdir <OUTDIR>
     ```
 
     Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -104,6 +104,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
         ```bash
         nextflow run nf-core/viralrecon \
             --input samplesheet.csv \
+            --outdir <OUTDIR> \
             --platform illumina \
             --protocol metagenomic \
             --genome 'MN908947.3' \
@@ -115,6 +116,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
         ```bash
         nextflow run nf-core/viralrecon \
             --input samplesheet.csv \
+            --outdir <OUTDIR> \
             --platform illumina \
             --protocol amplicon \
             --genome 'MN908947.3' \
@@ -129,6 +131,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
         ```bash
         nextflow run nf-core/viralrecon \
             --input samplesheet.csv \
+            --outdir <OUTDIR> \
             --platform nanopore \
             --genome 'MN908947.3' \
             --primer_set_version 3 \

conf/modules.config

@@ -17,22 +17,22 @@
 process {
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: 'copy',
+        mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
     withName: 'SAMPLESHEET_CHECK' {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*_versions.yml'
         ]
     }