nf-core · pinin4fjords · Nov 17, 2023 · Jun 14, 2023 · Jun 14, 2023 · Jun 14, 2023
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/rnaseq then the best place to ask is on the nf-core Slack [#rnaseq](https://nfcore.slack.com/channels/rnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/rnaseq then the best place to ask is on the nf-core Slack [#rnaseq](https://nfcore.slack.com/channels/rnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 
@@ -116,4 +118,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
@@ -232,16 +232,19 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
-  salmon:
-    name: Test Salmon with workflow parameters
+  pseudo:
+    name: Test Pseudoaligners with workflow parameters
     if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
         parameters:
-          - "--skip_qc"
-          - "--skip_alignment --skip_pseudo_alignment"
-          - "--salmon_index false --transcript_fasta false"
+          - "--pseudo_aligner salmon --skip_qc"
+          - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
+          - "--pseudo_aligner salmon --salmon_index false --transcript_fasta false"
+          - "--pseudo_aligner kallisto --skip_qc"
+          - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
+          - "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -280,6 +283,6 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - name: Run pipeline with Salmon and various parameters
+      - name: Run pipeline with Salmon or Kallisto and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
@@ -30,7 +30,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
           run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
-          profiles: test_full_aws,public_aws_ecr
+          profiles: test_full_aws
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",

diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
@@ -25,7 +25,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
           run_name: "aws_rnaseq_small"
-          profiles: test,public_aws_ecr
+          profiles: test
           parameters: |
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}"

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml
@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/[email protected]
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -3,5 +3,6 @@ lint:
   files_unchanged:
     - assets/email_template.html
     - assets/email_template.txt
-    - lib/NfcoreSchema.groovy
     - lib/NfcoreTemplate.groovy
+    - pyproject.toml
+  multiqc_config: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,67 @@
 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).
 
+## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [hmehlan](https://github.com/hmehlan)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Júlia Mir Pedrol](https://github.com/mirpedrol)
+- [Matthias Zepper](https://github.com/MatthiasZepper)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Steffen Möller](https://github.com/smoe)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [PR #1049](https://github.com/nf-core/rnaseq/pull/1049) - Display a warning when `--extra_star_align_args` are used with `--aligner star_rsem`
+- [PR #1051](https://github.com/nf-core/rnaseq/pull/1051) - Remove `public_aws_ecr` profile
+- [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
+- [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
+- [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
+- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage use of `--genome`
+- [PR #1078](https://github.com/nf-core/rnaseq/pull/1078) - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
+- [PR #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
+- [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
+- [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability
+- [PR #1106](https://github.com/nf-core/rnaseq/pull/1106) - Kallisto quantification
+- [PR #1107](https://github.com/nf-core/rnaseq/pull/1107) - Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage
+- [#976](https://github.com/nf-core/rnaseq/issues/976) - Add author and licenses for all custom scripts
+- [#1050](https://github.com/nf-core/rnaseq/issues/1050) - Provide custom prefix/suffix for summary files to avoid overwriting
+- [#1074](https://github.com/nf-core/rnaseq/issues/1074) - Enable quantification using StringTie AND a custom
+- [#1082](https://github.com/nf-core/rnaseq/issues/1082) - More informative error message for `filter_gtf_for_genes_in_genome.py`
+- [#1102](https://github.com/nf-core/rnaseq/issues/1102) - gene entries with empty transcript_id fields
+
+### Software dependencies
+
+| Dependency              | Old version | New version |
+| ----------------------- | ----------- | ----------- |
+| `fastqc`                | 0.11.9      | 0.12.1      |
+| `multiqc`               | 1.14        | 1.17        |
+| `ucsc-bedgraphtobigwig` | 377         | 445         |
+
+> **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.
+
+### Modules / Subworkflows
+
+| Script                   | Old name          | New name                    |
+| ------------------------ | ----------------- | --------------------------- |
+| `local/gtf_filter`       | `GTF_GENE_FILTER` | `GTF_FILTER`                |
+| `local/tx2gene`          | `SALMON_TX2GENE`  | `TX2GENE`                   |
+| `local/tximport`         | `SALMON_TXIMPORT` | `TXIMPORT`                  |
+| `local/quantify_salmon`  | `QUANTIFY_SALMON` | `QUANTIFY_PSEUDO_ALIGNMENT` |
+| `nf-core/kallisto_index` |                   | `KALLISTO_INDEX`            |
+| `nf-core/kallisto_quant` |                   | `KALLISTO_QUANT`            |
+
 ## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02
 
 ### Credits
@@ -21,7 +82,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [[#1011](https://github.com/nf-core/rnaseq/issues/1011)] - FastQ files from UMI-tools not being passed to fastp
-- [[#1018](https://github.com/nf-core/rnaseq/issues/1018)] - Ability to skip both alignment and pseudo-alignment to only run pre-processing QC steps.
+- [[#1018](https://github.com/nf-core/rnaseq/issues/1018)] - Ability to skip both alignment and pseudoalignment to only run pre-processing QC steps.
 - [PR #1016](https://github.com/nf-core/rnaseq/pull/1016) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #1025](https://github.com/nf-core/fetchngs/pull/1025) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
 - [PR #1038](https://github.com/nf-core/rnaseq/pull/1038) - Updated error log for count values when supplying `--additional_fasta`
@@ -769,7 +830,7 @@ Major novel changes include:
 - Added options to skip several steps
   - Skip trimming using `--skipTrimming`
   - Skip BiotypeQC using `--skipBiotypeQC`
-  - Skip Alignment using `--skipAlignment` to only use pseudo-alignment using Salmon
+  - Skip Alignment using `--skipAlignment` to only use pseudoalignment using Salmon
 
 ### Documentation updates
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -22,6 +22,8 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
 - [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)
 
   > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.
@@ -140,5 +142,8 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.