Merge branch 'dev' of github.com:ggabernet/nf-core-airrflow into dev

ggabernet · Mar 11, 2024 · 1244065 · 1244065
2 parents 72a02de + e1da721
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diff --git a/.github/CONTRIBUTING.md b/.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
 

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.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.

diff --git a/.github/workflows/branch.yml b/.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:

diff --git a/.github/workflows/linting.yml b/.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: |

diff --git a/.github/workflows/linting_comment.yml b/.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 }}

diff --git a/CHANGELOG.md b/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`
 
@@ -21,7 +21,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
 | multiqc    | 1.14        | 1.18        |
-| enchantr   | 0.9.0       | 0.10.0      |
+| enchantr   | 0.1.9       | 0.1.11      |
+| igblast    | 1.19.0      | 1.22.0      |
 
 ## [3.2.0] - 2023-10-27 Expecto patronum
 

diff --git a/README.md b/README.md
@@ -103,7 +103,7 @@ 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 \
@@ -119,7 +119,7 @@ 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 \

diff --git a/assets/multiqc_config.yml b/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>.
 

diff --git a/modules/local/changeo/changeo_assigngenes.nf b/modules/local/changeo/changeo_assigngenes.nf
@@ -3,7 +3,7 @@ process CHANGEO_ASSIGNGENES {
     label 'process_low'
     label 'immcantation'
 
-    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
         'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"

diff --git a/modules/local/changeo/changeo_convertdb_fasta.nf b/modules/local/changeo/changeo_convertdb_fasta.nf
@@ -4,7 +4,7 @@ process CHANGEO_CONVERTDB_FASTA {
     label 'immcantation'
 
 
-    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
         'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"

diff --git a/modules/local/changeo/changeo_creategermlines.nf b/modules/local/changeo/changeo_creategermlines.nf
@@ -4,7 +4,7 @@ process CHANGEO_CREATEGERMLINES {
     label 'immcantation'
 
 
-    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
         'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"

diff --git a/modules/local/changeo/changeo_makedb.nf b/modules/local/changeo/changeo_makedb.nf
@@ -4,8 +4,9 @@ process CHANGEO_MAKEDB {
     label 'immcantation'
 
 
-    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    //TODO: update mulled containers when available
         'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
         'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"
 

diff --git a/modules/local/changeo/changeo_parsedb_select.nf b/modules/local/changeo/changeo_parsedb_select.nf
@@ -4,7 +4,7 @@ process CHANGEO_PARSEDB_SELECT {
     label 'immcantation'
 
 
-    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
         'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"

diff --git a/modules/local/changeo/changeo_parsedb_split.nf b/modules/local/changeo/changeo_parsedb_split.nf
@@ -4,7 +4,7 @@ process CHANGEO_PARSEDB_SPLIT {
     label 'immcantation'
 
 
-    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
         'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"

diff --git a/modules/local/fetch_databases.nf b/modules/local/fetch_databases.nf
@@ -3,7 +3,7 @@ process FETCH_DATABASES {
     label 'process_low'
     label 'immcantation'
 
-    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
         'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"

diff --git a/modules/local/gunzip.nf b/modules/local/gunzip.nf
@@ -5,7 +5,7 @@ process GUNZIP {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'docker.io/biocontainers/biocontainers:v1.2.0_cv1' }"
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
     tuple val(meta), path(R1), path(R2)

diff --git a/modules/local/unzip_db.nf b/modules/local/unzip_db.nf
@@ -5,7 +5,7 @@ process UNZIP_DB {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'docker.io/biocontainers/biocontainers:v1.2.0_cv1' }"
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
     path(archive)

diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test