Merge pull request #19 from nf-core/dev

nf-core/isoseq pipeline release: v1.1.5

.editorconfig

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

.github/CONTRIBUTING.md

@@ -116,4 +116,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,9 +42,9 @@ 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 or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/isoseq _(eg. 1.1, 1.5, 1.8.2)_

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/isos
 
 - [ ] 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/isoseq/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/isoseq _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/isoseq/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/isoseq _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/awsfulltest.yml

@@ -14,18 +14,27 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
+        # TODO nf-core: You can customise AWS full pipeline tests as required
+        # Add full size test data (but still relatively small datasets for few samples)
+        # on the `test_full.config` test runs with only one set of parameters
+
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/isoseq/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/isoseq/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -12,18 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/isoseq/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/isoseq/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/isoseq'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/isoseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/isoseq ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.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

.github/workflows/clean-up.yml

@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies

.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

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier

CHANGELOG.md

@@ -3,6 +3,32 @@
 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).
 
+## v1.1.5 - Byzantium Buzzard [02/08/2023]
+
+Update the pipeline to nf-core 2.9.
+
+### `Added`
+
+### `Fixed`
+
+- Add gnu/sort to sort annotation before uLTRA index
+- Update citations
+- Add background to pipeline png
+  | Tool | Previous version | New version |
+  | -------------------- | ---------------- | ----------- |
+  | isoseq3 | 3.8.1 | 3.8.2 |
+  | lima | 2.6.0 | 2.7.1 |
+  | bamtools/convert | 2.5.1 | 2.5.2 |
+  | gstama/merge | 1.0.2 | 1.0.3 |
+  | uLTRA/index | 0.0.4.2 | 0.1 |
+  | uLTRA/align | 0.0.4.2 | 0.1 |
+  | samtools | 1.17 | 1.17 |
+  | gnu/sort | ---- | 8.25 |
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.1.4 - Teal Albatross [13/03/2023]
 
 ### `Added`

CITATIONS.md

@@ -36,7 +36,10 @@
 
   > Kuo, R.I., Cheng, Y., Zhang, R. et al. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics 21, 751 (2020).
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
@@ -55,5 +58,8 @@
 
 - [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.

README.md

@@ -3,13 +3,13 @@
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/isoseq/results)
 [![DOI](https://zenodo.org/badge/499464196.svg)](https://zenodo.org/badge/latestdoi/499464196)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![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/isoseq)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23isoseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/isoseq)[![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)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23isoseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/isoseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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
 
@@ -42,42 +42,55 @@ On release, automated continuous integration tests run the pipeline on a full-si
 9. Clean gene models ([`TAMA collapse`](https://github.com/GenomeRIK/tama))
 10. Merge annotations by sample ([`TAMA merge`](https://github.com/GenomeRIK/tama))
 
-## Quick Start
+## Usage
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
+> **Note**
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+> with `-profile test` before running the workflow on actual data.
 
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
+First, prepare a samplesheet with your input data that looks as follows:
 
-3. Download the pipeline and test it on a minimal dataset with a single command:
+`samplesheet.csv`:
 
-   ```bash
-   nextflow run nf-core/isoseq -profile test,YOURPROFILE --outdir <OUTDIR>
-   ```
+```csv
+sample,bam,pbi
+sample1,sample1.subreads.bam,sample1.subreads.bam.pbi
+```
 
-   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.
+Each row represents a pair of rqw subreads and it's associated pacbio index (pbi) file fastq files.
 
-   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
-   > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
-   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+Now, you can run the pipeline using:
 
-4. Start running your own analysis!
+```bash
+nextflow run nf-core/isoseq \
+   -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
+   --input samplesheet.csv \
+   --outdir <OUTDIR> \
+   --genome <GENOME NAME (e.g. GRCh37)> \
+   --primers <PRIMER FASTA>
+```
 
-   ```bash
-   nextflow run nf-core/isoseq --input samplesheet.csv --outdir <OUTDIR> --genome <GENOME NAME (e.g. GRCh37)> --primers <PRIMER FASTA> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
-   ```
+> **Warning:**
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
-## Documentation
+For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/isoseq/usage) and the [parameter documentation](https://nf-co.re/isoseq/parameters).
 
-The nf-core/isoseq pipeline comes with documentation about the pipeline [usage](https://nf-co.re/isoseq/usage), [parameters](https://nf-co.re/isoseq/parameters) and [output](https://nf-co.re/isoseq/output).
+## Pipeline output
+
+To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/isoseq/results) tab on the nf-core website pipeline page.
+For more details about the output files and reports, please refer to the
+[output documentation](https://nf-co.re/isoseq/output).
 
 ## Credits
 
 nf-core/isoseq was originally written by Sébastien Guizard.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-- Thanks to [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa), [Daniel Schreyer](https://github.com/DSchreyer) and [Gisela Gabernet](https://github.com/ggabernet) for their reviews and contributions
+- Thanks to [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa), [Daniel Schreyer](https://github.com/DSchreyer), [Gisela Gabernet](https://github.com/ggabernet) and [Maxime U Garcia](https://github.com/maxulysse) for their reviews and contributions
 - [Kristoffer Sahlin](https://github.com/ksahlin) for `uLTRA` and the help he provided
 - [Richard Kuo](https://github.com/GenomeRIK) ([Wobble Genomics](https://www.wobblegenomics.com/)) for his valuable advices on isoseq analysis
 - The Workpackage 2 of [GENE-SWitCH Project](https://www.gene-switch.eu/) for their fruitful discussions and remarks
@@ -95,15 +108,13 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- If you use  nf-core/isoseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+You can cite the `nf-core/isoseq` publication as follows:
 
-- [Isoseq3](https://github.com/PacificBiosciences/IsoSeq)
-- TAMA: Kuo, R.I., Cheng, Y., Zhang, R. et al. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics 21, 751 (2020). [10.1186/s12864-020-07123-7](https://doi.org/10.1186/s12864-020-07123-7)
-- Minimap2: Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100., Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. [10.1093/bioinformatics/btab705](https://doi.org/10.1093/bioinformatics/btab705)
-- uLTRA: Kristoffer Sahlin, Veli Mäkinen, Accurate spliced alignment of long RNA sequencing reads, Bioinformatics, Volume 37, Issue 24, 15 December 2021, Pages 4643–4651. [10.1093/bioinformatics/btab540](https://doi.org/10.1093/bioinformatics/btab540)
-- Samtools: Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H, Twelve years of SAMtools and BCFtools, GigaScience (2021) 10(2) giab008. [10.1093/gigascience/giab007](https://doi.org/10.1093/gigascience/giab007)
-- MultiQC: Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller, MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, Volume 32, Issue 19, 1 October 2016, Pages 3047–3048. [10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354)
-- samtools: Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H, Twelve years of SAMtools and BCFtools, GigaScience (2021) 10(2) [10.1093/gigascience/giab008](https://academic.oup.com/gigascience/article/10/2/giab008/6137722?login=false)
+> **nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing**
+>
+> Sébastien Guizard, Katarzyna Miedzinska, Jacqueline Smith, Jonathan Smith, Richard I Kuo, Megan Davey, Alan Archibald & Mick Watson.
+>
+> Bioinformatics, Volume 39, Issue 5, May 2023. doi: [10.1093/bioinformatics/btad150](https://doi.org/10.1093/bioinformatics/btad150)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.