Merge pull request #282 from nf-core/dev

Release 3.2.0

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.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/airrflow then the best place to ask is on the nf-core Slack [#airrflow](https://nfcore.slack.com/channels/airrflow) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/airrflow then the best place to ask is on the nf-core Slack [#airrflow](https://nfcore.slack.com/channels/airrflow) 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)

.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)_

.github/workflows/awsfulltest.yml

@@ -14,18 +14,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        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/airrflow/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/airrflow/results-${{ 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: seqeralabs/action-tower-launch@v1
+        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/airrflow/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/airrflow/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/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
@@ -46,9 +46,10 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
-        profile: ["test_tcr", "test_no_umi", "test_nocluster", "test_fetchimgt", "test_assembled"]
+        profile:
+          ["test_tcr", "test_no_umi", "test_nocluster", "test_fetchimgt", "test_assembled_hs", "test_assembled_mm"]
       fail-fast: false
     steps:
       - name: Check out pipeline code

.github/workflows/ci_immcantation.yml

@@ -1,9 +1,6 @@
 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:
-    branches:
-      - dev
   pull_request:
     branches-ignore:
       - "master"
@@ -23,9 +20,14 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
-        profile: ["test_assembled_immcantation_devel", "test_raw_immcantation_devel"]
+        profile:
+          [
+            "test_assembled_immcantation_devel_hs",
+            "test_assembled_immcantation_devel_mm",
+            "test_raw_immcantation_devel",
+          ]
       fail-fast: false
     steps:
       - name: Check out pipeline code

.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

.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 }}
+          #

.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

.nf-core.yml

@@ -1,4 +1,6 @@
 lint:
   files_exist:
     - conf/igenomes.config
+  multiqc_config:
+    - report_comment
 repository_type: pipeline

CHANGELOG.md

@@ -3,7 +3,37 @@
 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"
+## [3.2.0] - 2023-10-27 Expecto patronum
+
+### `Added`
+
+- [#268](https://github.com/nf-core/airrflow/pull/268) Added parameters for FindThreshold in `modules.config`.
+- [#268](https://github.com/nf-core/airrflow/pull/268) Validate samplesheet also for `assembled` samplesheet.
+- [#259](https://github.com/nf-core/airrflow/pull/259) Update to `EnchantR v0.1.3`.
+- [#266](https://github.com/nf-core/airrflow/pull/266) Added clonal reports tables to final report folder.
+- [#266](https://github.com/nf-core/airrflow/pull/266) Added processes to include sampleID to filename in assembled workflow to keep it unique.
+- [#276](https://github.com/nf-core/airrflow/pull/276) Parametrize FindThreshold Report and Presto Buildconsensus UMI.
+- [#281](https://github.com/nf-core/airrflow/pull/281) Update to nf-core tools v2.10.
+
+### `Fixed`
+
+- [#268](https://github.com/nf-core/airrflow/pull/268) Allows for uppercase and lowercase locus in samplesheet `pcr_target_locus`.
+- [#259](https://github.com/nf-core/airrflow/pull/259) Samplesheet only allows data from one species.
+- [#259](https://github.com/nf-core/airrflow/pull/259) Introduced fix for a too long command with hundreds of datasets.
+- [#266](https://github.com/nf-core/airrflow/pull/266) Convert samplesheet required columns to strings when needed.
+- [#284](https://github.com/nf-core/bcellmagic/pull/284): Use cached IMGT and IgBlast reference data by default.
+
+### `Dependencies`
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| r-enchantr | 0.1.2       | 0.1.9       |
+| r-alakazam | 1.2.1       | 1.3.0       |
+| r-shazam   | 1.1.0       | 1.2.0       |
+| r-dowser   | 1.2.0       | 2.0.0       |
+| fastqc     | 0.11.9      | 0.12.1      |
+
+## [3.1.0] - 2023-06-05 "Protego"
 
 ### `Added`
 
@@ -195,7 +225,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#114](https://github.com/nf-core/bcellmagic/pull/114): Added Bcellmagic html report.
 - [#114](https://github.com/nf-core/bcellmagic/pull/114): Improved documentation on amplicon protocol support.
 - [#115](https://github.com/nf-core/bcellmagic/pull/115): Improved output file structure and documentation.
-- [#124](https://github.com/nf-core/bcellmagic/pull/124): Template update to nf-core tools v2.0.1
+- [#124](https://github.com/nf-core/bcellmagic/pull/124): Template update to nf-core tools v2.0.1.
 
 ### `Fixed`
 

CITATIONS.md

@@ -12,6 +12,44 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
+- [Fastp](https://doi.org/10.1093/bioinformatics/bty560)
+
+  > 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.
+
+- [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.
+
+- [SHazaM, Change-O](https://doi.org/10.1093/bioinformatics/btv359)
+
+  > Gupta, N. T., Vander Heiden, J. A., Uduman, M., Gadala-Maria, D., Yaari, G., & Kleinstein, S. H. (2015). Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. Bioinformatics, 31(20), 3356–3358.
+
+- [Alakazam](https://doi.org/10.1126/scitranslmed.3008879)
+
+  > 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.
+
 - [Fastp](https://doi.org/10.1093/bioinformatics/bty560)
 
   > 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.
@@ -68,5 +106,8 @@
 
 - [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.