Bump versions and update software versions

.github/CONTRIBUTING.md

@@ -9,9 +9,8 @@ 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 ;)
 
-:::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)).
-:::
+> [!NOTE]
+> 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
 
@@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
-receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/airr
 - [ ] 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>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/branch.yml

@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v2
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

.github/workflows/linting.yml

@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: "pip"
@@ -32,12 +32,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -60,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v3
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## [3.3.0dev] -
+## [3.3.0] -
 
 ### `Added`
 
@@ -16,14 +16,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - [#294](https://github.com/nf-core/airrflow/pull/294) Removed optional output from FilterQuality to not fail silently
 - [#293](https://github.com/nf-core/airrflow/pull/293) Clonal_threshold is validated to be 'auto' or number greater than zero
-- [#295](https://github.com/nf-core/airrflow/pull/295) Fixed airrflow report sequence plot and add path to clonal analysis reports.
+- [#295](https://github.com/nf-core/airrflow/pull/295) Fixed airrflow report sequence plot and add path to clonal analysis reports
+- [#310](https://github.com/nf-core/airrflow/pull/310) Bump versions to 3.3.0, update containers and software versions
 
 ### `Dependencies`
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| multiqc    | 1.14        | 1.18        |
-| enchantr   | 0.9.0       | 0.10.0      |
+| multiqc    | 1.19        | 1.21        |
+| enchantr   | 0.1.9       | 0.1.11      |
+| igblast    | 1.19.0      | 1.22.0      |
 
 ## [3.2.0] - 2023-10-27 Expecto patronum
 

README.md

@@ -110,7 +110,7 @@ A typical command to run the pipeline from **bulk raw fastq files** is:
 
 ```bash
 nextflow run nf-core/airrflow \
--r 3.2.0 \
+-r <release> \
 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
 --mode fastq \
 --input input_samplesheet.tsv \
@@ -138,7 +138,7 @@ A typical command to run the pipeline from **single-cell AIRR rearrangement tabl
 
 ```bash
 nextflow run nf-core/airrflow \
--r 3.2.0 \
+-r <release> \
 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
 --input input_samplesheet.tsv \
 --mode assembled \

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/airrflow/tree/dev" target="_blank">nf-core/airrflow</a>
+  This report has been generated by the <a href="https://github.com/nf-core/airrflow/releases/tag/3.3.0" target="_blank">nf-core/airrflow</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/airrflow" target="_blank">documentation</a>.
 

assets/repertoire_comparison.Rmd

@@ -16,7 +16,7 @@ output:
 
 
 ---
-title: "Repertoire analysis"
+title: "Airrflow results summary report"
 subtitle: "Interactive summary report produced by the nf-core/airrflow pipeline"
 date: '`r format(Sys.Date(), "%B %d, %Y")`'
 output: html_document
@@ -48,7 +48,7 @@ datadir <- "."
 
 ```
 
-# Airrflow results
+# AIRR repertoire results
 
 The repertoires per subject after clonal analysis can be found in the
 subdirectory [clonal_analysis/define_clones/all_reps_clone_report/repertoires](clonal_analysis/define_clones/all_reps_clone_report/repertoires).
@@ -98,7 +98,7 @@ tryCatch( {
 )
 ```
 
-## Filtering and clonal analysis steps
+## V(D)J gene assignment and QC
 
 Number of sequences for each of the samples after each of the downstream filtering and clonal analysis steps.
 The full table can be found under [Table_sequences_assembled](repertoire_comparison/Sequence_numbers_summary/Table_sequences_assembled.tsv).

conf/clontech_umi_bcr.config

@@ -37,4 +37,5 @@ params {
     primer_r1_maxerror = 0.2
     assemblepairs_sequential = true
     primer_consensus = 0.6
+    isotype_column = 'cregion'
 }

conf/modules.config

@@ -542,7 +542,6 @@ process {
         ]
         ext.args = ['outname':'', 'model':'hierarchical',
                     'method':'nt', 'linkage':'single',
-                    'skip_convergence':true,
                     'min_n':30]
     }
 
@@ -554,7 +553,6 @@ process {
         ]
         ext.args = ['outname':'', 'model':'hierarchical',
                     'method':'nt', 'linkage':'single',
-                    'skip_convergence':false,
                     'min_n':30]
     }
 

conf/nebnext_umi_bcr.config

@@ -35,4 +35,5 @@ params {
     cregion_maxlen = 100
     cregion_maxerror = 0.3
     cregion_mask_mode = 'tag'
+    isotype_column = 'cregion'
 }

conf/test.config

@@ -34,6 +34,7 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
+    isotype_column = 'c_primer'
 }
 
 process{

conf/test_clontech_umi.config

@@ -27,5 +27,6 @@ params {
     igblast_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
 
     clonal_threshold = 0.1
+    skip_lineage = true
 
 }

conf/test_fetchimgt.config

@@ -33,6 +33,7 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
+    isotype_column = 'c_primer'
 }
 
 process{

conf/test_nebnext_umi.config

@@ -28,5 +28,6 @@ params {
     igblast_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
 
     clonal_threshold = 0.1
+    skip_lineage = true
 
 }

conf/test_no_umi.config

@@ -24,6 +24,7 @@ params {
     vprimer_start = 4
     primer_revpr = true
     umi_length = 0
+    isotype_column = 'c_primer'
 
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-no-umi/Metadata_test-no-umi_airr.tsv'

conf/test_nocluster.config

@@ -36,6 +36,7 @@ params {
     cluster_sets = false
     index_file = true
     clonal_threshold = 0.15
+    isotype_column = 'c_primer'
 }
 
 process{

conf/test_raw_immcantation_devel.config

@@ -36,6 +36,7 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
+    isotype_column = 'c_primer'
 }
 
 process{

conf/test_tcr.config

@@ -25,6 +25,7 @@ params {
     library_generation_method = 'dt_5p_race_umi'
     cprimer_position = 'R1'
     clonal_threshold = 0
+    skip_lineage = true
 
 
     // Input data