Merge pull request #876 from nf-core/dev

Dev -> Master for v3.9 release

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/rnaseq _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 --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/ci.yml

@@ -10,7 +10,6 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  CAPSULE_LOG: none
 
 jobs:
   test:
@@ -20,27 +19,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Nextflow versions
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
+        NXF_VER:
+          - "21.10.3"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.NXF_VER }}
-          # Uncomment only if the edge release is more recent than the latest stable release
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
         run: |

.github/workflows/linting.yml

@@ -35,22 +35,48 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Check code lints with Black
+        uses: psf/black@stable
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@v3
         with:
-          python-version: "3.6"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies

.nf-core.yml

@@ -4,13 +4,3 @@ lint:
     - assets/email_template.html
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
-update:
-  nf-core/modules:
-    rseqc/bamstat: "e745e167c1020928ef20ea1397b6b4d230681b4d"
-    rseqc/inferexperiment: "e745e167c1020928ef20ea1397b6b4d230681b4d"
-    rseqc/innerdistance: "e745e167c1020928ef20ea1397b6b4d230681b4d"
-    rseqc/junctionannotation: "e745e167c1020928ef20ea1397b6b4d230681b4d"
-    rseqc/junctionsaturation: "e745e167c1020928ef20ea1397b6b4d230681b4d"
-    rseqc/readdistribution: "e745e167c1020928ef20ea1397b6b4d230681b4d"
-    rseqc/readduplication: "e745e167c1020928ef20ea1397b6b4d230681b4d"
-    rseqc/tin: "4dbc166a7c30e963511fb5c9870fbcaa158a53a9"

CHANGELOG.md

@@ -3,6 +3,41 @@
 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).
 
+## [[3.9](https://github.com/nf-core/rnaseq/releases/tag/3.9)] - 2022-09-30
+
+### Enhancements & fixes
+
+- [[#746](https://github.com/nf-core/rnaseq/issues/746)] - Add `tin.py` output to MultiQC report
+- [[#841](https://github.com/nf-core/rnaseq/issues/841)] - Turn `--deseq2_vst` on by default
+- [[#853](https://github.com/nf-core/rnaseq/issues/853)] - Pipeline fails at email step: Failed to invoke `workflow.onComplete` event handler
+- [[#857](https://github.com/nf-core/rnaseq/issues/857)] - Missing parameter required by StringTie if using STAR as aligner
+- [[#862](https://github.com/nf-core/rnaseq/issues/862)] - Filter samples that have no reads after trimming
+- [[#864](https://github.com/nf-core/rnaseq/issues/864)] - Pre-process transcripts fasta when using `--gencode`
+- Expose additional arguments to UMI-tools as pipeline params: `--umitools_bc_pattern2` is required if the UMI is located on read 2. `--umitools_umi_separator` will often be needed in conjunction with `--skip_umi_extract` as most other tools such as Illumina's `BCL Convert` use a colon instead of an underscore to separate the UMIs. The `--umitools_grouping_method` allows to fine-tune handling of similar but non-identical UMIs.
+- Updated pipeline template to [nf-core/tools 2.5.1](https://github.com/nf-core/tools/releases/tag/2.5.1)
+
+### Parameters
+
+| Old parameter | New parameter                |
+| ------------- | ---------------------------- |
+|               | `--umitools_bc_pattern2`     |
+|               | `--umitools_umi_separator`   |
+|               | `--umitools_grouping_method` |
+
+### Software dependencies
+
+Note, since the pipeline is now 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.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `hisat2`   | 2.2.0       | 2.2.1       |
+| `multiqc`  | 1.11        | 1.13        |
+| `picard`   | 2.26.10     | 2.27.4      |
+
+> **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 version information isn't present.
+
 ## [[3.8.1](https://github.com/nf-core/rnaseq/releases/tag/3.8.1)] - 2022-05-27
 
 - [[#834](https://github.com/nf-core/rnaseq/issues/834)] - `nf-core download` fails with version 3.8 of the pipeline

CITATION.cff

@@ -0,0 +1,56 @@
+cff-version: 1.2.0
+message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
+authors:
+  - family-names: Ewels
+    given-names: Philip
+  - family-names: Peltzer
+    given-names: Alexander
+  - family-names: Fillinger
+    given-names: Sven
+  - family-names: Patel
+    given-names: Harshil
+  - family-names: Alneberg
+    given-names: Johannes
+  - family-names: Wilm
+    given-names: Andreas
+  - family-names: Ulysse Garcia
+    given-names: Maxime
+  - family-names: Di Tommaso
+    given-names: Paolo
+  - family-names: Nahnsen
+    given-names: Sven
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+  type: article
+  authors:
+    - family-names: Ewels
+      given-names: Philip
+    - family-names: Peltzer
+      given-names: Alexander
+    - family-names: Fillinger
+      given-names: Sven
+    - family-names: Patel
+      given-names: Harshil
+    - family-names: Alneberg
+      given-names: Johannes
+    - family-names: Wilm
+      given-names: Andreas
+    - family-names: Ulysse Garcia
+      given-names: Maxime
+    - family-names: Di Tommaso
+      given-names: Paolo
+    - family-names: Nahnsen
+      given-names: Sven
+  doi: 10.1038/s41587-020-0439-x
+  journal: nature biotechnology
+  start: 276
+  end: 278
+  title: "The nf-core framework for community-curated bioinformatics pipelines."
+  issue: 3
+  volume: 38
+  year: 2020
+  url: https://dx.doi.org/10.1038/s41587-020-0439-x

README.md

@@ -1,19 +1,14 @@
 # ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_light.png#gh-light-mode-only) ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_dark.png#gh-dark-mode-only)
 
-[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8)](https://doi.org/10.5281/zenodo.1400710)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/)
-[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
-[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnaseq)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?logo=slack)](https://nfcore.slack.com/channels/rnaseq)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
-[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -69,7 +64,7 @@ The SRA download functionality has been removed from the pipeline (`>=3.2`) and
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-   ```console
+   ```bash
    nextflow run nf-core/rnaseq -profile test,YOURPROFILE --outdir <OUTDIR>
    ```
 
@@ -82,13 +77,13 @@ The SRA download functionality has been removed from the pipeline (`>=3.2`) and
 
 4. Start running your own analysis!
 
-   ```console
+   ```bash
    nextflow run nf-core/rnaseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
    - An executable Python script called [`fastq_dir_to_samplesheet.py`](https://github.com/nf-core/rnaseq/blob/master/bin/fastq_dir_to_samplesheet.py) has been provided if you would like to auto-create an input samplesheet based on a directory containing FastQ files **before** you run the pipeline (requires Python 3 installed locally) e.g.
 
-     ```console
+     ```bash
      wget -L https://raw.githubusercontent.com/nf-core/rnaseq/master/bin/fastq_dir_to_samplesheet.py
      ./fastq_dir_to_samplesheet.py <FASTQ_DIR> samplesheet.csv --strandedness reverse
      ```