Merge pull request #279 from nf-core/dev

Dev -> Master for 2.3.1 release
nf-core · Feb 15, 2022 · 97bebf8 · 97bebf8
2 parents fc9fece + ee7c22b
commit 97bebf8
Show file tree

Hide file tree

Showing 142 changed files with 1,719 additions and 1,435 deletions.
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,4 +1,3 @@
-
 name: Bug report
 description: Report something that is broken or incorrect
 labels: bug

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -32,3 +32,6 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}"
             }
           profiles: test_full_${{ matrix.platform }},aws_tower
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -25,3 +25,6 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -43,4 +43,3 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -12,9 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
@@ -51,9 +49,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -65,13 +61,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
+      - uses: actions/setup-node@v2
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.yamllint.yml
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -87,7 +81,7 @@ jobs:
             * Install `yaml-lint`
                 * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
             * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
                 * Fix any reported errors in your YAML files
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
@@ -142,4 +136,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -1,4 +1,3 @@
-
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -27,4 +26,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore                 # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow                 # Highlight indentation level
+    - streetsidesoftware.code-spell-checker  # Spelling checker for source code
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -4,3 +4,8 @@ lint:
     - assets/email_template.html
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - lib/NfcoreSchema.groovy
diff --git a/.yamllint.yml b/.yamllint.yml
@@ -0,0 +1,5 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,19 @@
 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).
 
+## [[2.3.1](https://github.com/nf-core/viralrecon/releases/tag/2.3.1)] - 2022-02-15
+
+### Enhancements & fixes
+
+* [[#277](https://github.com/nf-core/viralrecon/issues/277)] - Misuse of rstrip in make_variants_long_table.py script
+
+### Software dependencies
+
+| Dependency                    | Old version | New version |
+|-------------------------------|-------------|-------------|
+| `mosdepth`                    | 0.3.2       | 0.3.3       |
+| `pangolin`                    | 3.1.19      | 3.1.20      |
+
 ## [[2.3](https://github.com/nf-core/viralrecon/releases/tag/2.3)] - 2022-02-04
 
 ### :warning: Major enhancements
@@ -38,9 +51,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 |                               | `--consensus_caller`                  |
 | `--callers`                   | `--variant_caller`                    |
 
-> **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.
+> **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.
 
 ### Software dependencies
 
@@ -66,9 +81,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `tabix`                       | 0.2.6       | 1.11        |
 | `vcflib`                      |             | 1.0.2       |
 
-> **NB:** Dependency has been __updated__ if both old and new version information is present.
-> **NB:** Dependency has been __added__ if just the new version information is present.
-> **NB:** Dependency has been __removed__ if new version information isn't present.
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
 
 ## [[2.2](https://github.com/nf-core/viralrecon/releases/tag/2.2)] - 2021-07-29
 
@@ -89,9 +106,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `pangolin`                    | 3.0.5       | 3.1.7       |
 | `samtools`                    | 1.10        | 1.12        |
 
-> **NB:** Dependency has been __updated__ if both old and new version information is present.
-> **NB:** Dependency has been __added__ if just the new version information is present.
-> **NB:** Dependency has been __removed__ if new version information isn't present.
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
 
 ## [[2.1](https://github.com/nf-core/viralrecon/releases/tag/2.1)] - 2021-06-15
 
@@ -117,9 +136,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `--public_data_ids`           |                                       |
 | `--skip_sra_fastq_download`   |                                       |
 
-> **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.
+> **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.
 
 ### Software dependencies
 
@@ -130,9 +151,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `nextclade_js`                | 0.14.2      | 0.14.4      |
 | `pangolin`                    | 2.4.2       | 3.0.5       |
 
-> **NB:** Dependency has been __updated__ if both old and new version information is present.
-> **NB:** Dependency has been __added__ if just the new version information is present.
-> **NB:** Dependency has been __removed__ if new version information isn't present.
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
 
 ## [[2.0](https://github.com/nf-core/viralrecon/releases/tag/2.0)] - 2021-05-13
 
@@ -232,9 +255,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `--unqualified_percent_limit` |                                       |
 | `--varscan2_strand_filter`    |                                       |
 
-> **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.
+> **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.
 
 ### Software dependencies
 
@@ -283,9 +308,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `varscan`                     | 2.4.4       |             |
 | `vg`                          | 1.24.0      |             |
 
-> **NB:** Dependency has been __updated__ if both old and new version information is present.
-> **NB:** Dependency has been __added__ if just the new version information is present.
-> **NB:** Dependency has been __removed__ if new version information isn't present.
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
 
 ## [[1.1.0](https://github.com/nf-core/viralrecon/releases/tag/1.1.0)] - 2020-06-23
 
@@ -338,23 +365,23 @@ This pipeline is a re-implementation of the [SARS_Cov2_consensus-nf](https://git
 
 ### Pipeline summary
 
-1. Download samples via SRA, ENA or GEO ids ([`ENA FTP`](https://ena-docs.readthedocs.io/en/latest/retrieval/file-download.html), [`parallel-fastq-dump`](https://github.com/rvalieris/parallel-fastq-dump); *if required*)
-2. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html); *if required*)
+1. Download samples via SRA, ENA or GEO ids ([`ENA FTP`](https://ena-docs.readthedocs.io/en/latest/retrieval/file-download.html), [`parallel-fastq-dump`](https://github.com/rvalieris/parallel-fastq-dump); _if required_)
+2. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html); _if required_)
 3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 4. Adapter trimming ([`fastp`](https://github.com/OpenGene/fastp))
 5. Variant calling
     1. Read alignment ([`Bowtie 2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
     2. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
-    3. Primer sequence removal ([`iVar`](https://github.com/andersen-lab/ivar); *amplicon data only*)
-    4. Duplicate read marking ([`picard`](https://broadinstitute.github.io/picard/); *removal optional*)
+    3. Primer sequence removal ([`iVar`](https://github.com/andersen-lab/ivar); _amplicon data only_)
+    4. Duplicate read marking ([`picard`](https://broadinstitute.github.io/picard/); _removal optional_)
     5. Alignment-level QC ([`picard`](https://broadinstitute.github.io/picard/), [`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
-    6. Choice of multiple variant calling and consensus sequence generation routes ([`VarScan 2`](http://dkoboldt.github.io/varscan/), [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/) *||* [`iVar variants and consensus`](https://github.com/andersen-lab/ivar) *||* [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/))
+    6. Choice of multiple variant calling and consensus sequence generation routes ([`VarScan 2`](http://dkoboldt.github.io/varscan/), [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/) _||_ [`iVar variants and consensus`](https://github.com/andersen-lab/ivar) _||_ [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/))
         * Variant annotation ([`SnpEff`](http://snpeff.sourceforge.net/SnpEff.html), [`SnpSift`](http://snpeff.sourceforge.net/SnpSift.html))
         * Consensus assessment report ([`QUAST`](http://quast.sourceforge.net/quast))
 6. _De novo_ assembly
-    1. Primer trimming ([`Cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html); *amplicon data only*)
+    1. Primer trimming ([`Cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html); _amplicon data only_)
     2. Removal of host reads ([`Kraken 2`](http://ccb.jhu.edu/software/kraken2/))
-    3. Choice of multiple assembly tools ([`SPAdes`](http://cab.spbu.ru/software/spades/) *||* [`metaSPAdes`](http://cab.spbu.ru/software/meta-spades/) *||* [`Unicycler`](https://github.com/rrwick/Unicycler) *||* [`minia`](https://github.com/GATB/minia))
+    3. Choice of multiple assembly tools ([`SPAdes`](http://cab.spbu.ru/software/spades/) _||_ [`metaSPAdes`](http://cab.spbu.ru/software/meta-spades/) _||_ [`Unicycler`](https://github.com/rrwick/Unicycler) _||_ [`minia`](https://github.com/GATB/minia))
         * Blast to reference genome ([`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch))
         * Contiguate assembly ([`ABACAS`](https://www.sanger.ac.uk/science/tools/pagit))
         * Assembly report ([`PlasmidID`](https://github.com/BU-ISCIII/plasmidID))