Merge pull request #262 from nf-core/dev

3.1.0 release: Template update and minor bugfixes

.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
 
 [*.json]

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -45,6 +45,6 @@ body:
         * Nextflow version _(eg. 22.10.1)_
         * 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/airrflow _(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/airr
 
 - [ ] 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/airrflow/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/airrflow _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/airrflow/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/airrflow _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

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v1
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/awstest.yml

@@ -12,7 +12,7 @@ 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@v1
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/airrflow'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/airrflow ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/airrflow ]] && [[ $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

@@ -48,11 +48,11 @@ jobs:
         NXF_VER:
           - "22.10.1"
           - "latest-everything"
-        profile: ["test_tcr", "test_no_umi", "test_nocluster", "test_fetchimgt", "test_assembled", "test_igblast"]
+        profile: ["test_tcr", "test_no_umi", "test_nocluster", "test_fetchimgt", "test_assembled"]
       fail-fast: false
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/ci_immcantation.yml

@@ -1,4 +1,4 @@
-name: nf-core CI
+name: nf-core CI immcantation
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   push:
@@ -29,7 +29,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.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

.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 +3,30 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [3.1] - 2023-06-05 "Protego"
+
+### `Added`
+
+- [#250](https://github.com/nf-core/airrflow/pull/250) Back to `dev`.
+- [#256](https://github.com/nf-core/airrflow/pull/256) Merge template updates to nf-core tools 2.8.
+- [#263](https://github.com/nf-core/airrflow/pull/263) Bump versions to 3.1.
+
+### `Fixed`
+
+- [#250](https://github.com/nf-core/airrflow/pull/250) Fixed log parsing with `removeprefix` instead of `lstrip`.
+- [#258](https://github.com/nf-core/airrflow/pull/258) Fixes to plotly plots in report sometimes not rendering.
+- [#258](https://github.com/nf-core/airrflow/pull/258) Remove direct call to Igblast in favor of a fix in ChangeO.
+- [#258](https://github.com/nf-core/airrflow/pull/258) Added check for whitespaces in certain columns in samplesheet.
+- [#258](https://github.com/nf-core/airrflow/pull/258) Added missing Immcantation references in Airrflow report.
+
+### `Dependencies`
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| r-enchantr | 0.1.1       | 0.1.2       |
+| multiqc    | 1.13        | 1.14        |
+| fastp      | 0.23.2      | 0.23.4      |
+
 ## [3.0] - 2023-03-20 "Portus"
 
 ### `Added`

CITATIONS.md

@@ -16,10 +16,6 @@
 
   > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics. 2018 Sept 1; 34(17):i884–i890. doi: 10.1093/bioinformatics/bty560.
 
-- [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.
-
 - [pRESTO](https://doi.org/10.1093/bioinformatics/btu138)
 
   > Vander Heiden, J. A., Yaari, G., Uduman, M., Stern, J. N. H., O’Connor, K. C., Hafler, D. A., … Kleinstein, S. H. (2014). pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics, 30(13), 1930–1932.
@@ -32,9 +28,30 @@
 
   > Stern, J. N. H., Yaari, G., Vander Heiden, J. A., Church, G., Donahue, W. F., Hintzen, R. Q., … O’Connor, K. C. (2014). B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Science Translational Medicine, 6(248).
 
+- [SCOPer](https://doi.org/10.1093/bioinformatics/bty235)
+
+  > Nouri N, Kleinstein S (2018). “A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.” Bioinformatics, i341-i349.
+
+  > Nouri N, Kleinstein S (2020). “Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.” PLOS Computational Biology, 16(6), e1007977.
+
+  > Gupta N, Adams K, Briggs A, Timberlake S, Vigneault F, Kleinstein S (2017). “Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data.” The Journal of Immunology, 2489-2499.
+
+- [Dowser](https://doi.org/10.1371/journal.pcbi.1009885)
+
+  > Hoehn K, Pybus O, Kleinstein S (2022). “Phylogenetic analysis of migration, differentiation, and class switching in B cells.” PLoS Computational Biology.
+
+- [IgPhyML](https://www.pnas.org/doi/10.1073/pnas.1906020116)
+
+  > Hoehn K, Van der Heiden J, Zhou J, Lunter G, Pybus O, Kleinstein S (2019). “Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.” PNAS.
+
 - [TIgGER](https://doi.org/10.1073/pnas.1417683112)
+
   > Gadala-maria, D., Yaari, G., Uduman, M., & Kleinstein, S. H. (2015). Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proceedings of the National Academy of Sciences, 112(8), 1–9.
 
+- [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
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -8,6 +8,7 @@
 [![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/airrflow)
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23airrflow-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/airrflow)
 [![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)
@@ -73,26 +74,29 @@ nf-core/airrflow allows the end-to-end processing of BCR and TCR bulk and single
 - Custom repertoire analysis pipeline report (`Alakazam`).
 - Aggregate QC reports (`MultiQC`).
 
-## 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, ensure that the pipeline tests run on your infrastructure:
 
-3. Download the pipeline and test it on a minimal dataset with a single command:
+```bash
+nextflow run nf-core/airrflow -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute> --outdir <OUTDIR>
+```
 
-   ```console
-   nextflow run nf-core/airrflow -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute> --outdir <OUTDIR>
-   ```
+To run on your data, prepare a tab-separated samplesheet with your input data. Depending on the input data type (bulk or single-cell, raw reads or assembled reads) the input samplesheet will vary. Please follow the [documentation on samplesheets](https://nf-co.re/airrflow/usage#input-samplesheet) for more details. An example samplesheet for running the pipeline on raw BCR / TCR sequencing data looks as follows:
 
-   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.
+| sample_id | filename_R1                     | filename_R2                     | filename_I1                     | subject_id | species | pcr_target_locus | tissue | sex    | age | biomaterial_provider | single_cell | intervention   | collection_time_point_relative | cell_subset  |
+| --------- | ------------------------------- | ------------------------------- | ------------------------------- | ---------- | ------- | ---------------- | ------ | ------ | --- | -------------------- | ----------- | -------------- | ------------------------------ | ------------ |
+| sample01  | sample1_S8_L001_R1_001.fastq.gz | sample1_S8_L001_R2_001.fastq.gz | sample1_S8_L001_I1_001.fastq.gz | Subject02  | human   | IG               | blood  | NA     | 53  | sequencing_facility  | FALSE       | Drug_treatment | Baseline                       | plasmablasts |
+| sample02  | sample2_S8_L001_R1_001.fastq.gz | sample2_S8_L001_R2_001.fastq.gz | sample2_S8_L001_I1_001.fastq.gz | Subject02  | human   | TR               | blood  | female | 78  | sequencing_facility  | FALSE       | Drug_treatment | Baseline                       | plasmablasts |
 
-   > - 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.
+Each row represents a sample with fastq files (paired-end).
 
-4. Start running your own analysis!
+A typical command to run the pipeline is:
 
 ```bash
 nextflow run nf-core/airrflow \
@@ -107,15 +111,22 @@ nextflow run nf-core/airrflow \
 --outdir ./results
 ```
 
-See [usage docs](https://nf-co.re/airrflow/usage) for all of the available options when running the pipeline.
+> **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).
+
+For more details, please refer to the [usage documentation](https://nf-co.re/airrflow/usage) and the [parameter documentation](https://nf-co.re/airrflow/parameters).
 
-## Documentation
+## Pipeline output
 
-The nf-core/airrflow pipeline comes with documentation about the pipeline [usage](https://nf-co.re/airrflow/usage), [parameters](https://nf-co.re/airrflow/parameters) and [output](https://nf-co.re/airrflow/output).
+To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/airrflow/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/airrflow/output).
 
 ## Credits
 
-nf-core/airrflow was written by [Gisela Gabenet](https://github.com/ggabernet), [Susanna Marquez](https://github.com/ssnn-airr), [Alexander Peltzer](@apeltzer) and [Simon Heumos](@subwaystation).
+nf-core/airrflow was written by [Gisela Gabernet](https://github.com/ggabernet), [Susanna Marquez](https://github.com/ssnn-airr), [Alexander Peltzer](@apeltzer) and [Simon Heumos](@subwaystation).
 
 Further contributors to the pipeline are: