Merge pull request nf-core#281 from ggabernet/small-fixes

small fixes
ggabernet · Oct 23, 2023 · 9a2031b · 9a2031b
2 parents 9743661 + 35d63e1
commit 9a2031b
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

diff --git a/.github/workflows/release-announcments.yml b/.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 }}
+          #
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#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.
-- [#279](https://github.com/nf-core/airrflow/pull/279) Update to nf-core tools v2.10.
+- [#281](https://github.com/nf-core/airrflow/pull/281) Update to nf-core tools v2.10.
 
 ### `Fixed`
 
@@ -27,7 +27,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| r-enchantr | 0.1.2       | 0.1.5       |
+| r-enchantr | 0.1.2       | 0.1.7       |
+| 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"
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -12,7 +12,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online 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)
 

diff --git a/README.md b/README.md
@@ -26,7 +26,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-nf-core/airrflow allows the end-to-end processing of BCR and TCR bulk and single cell targeted sequencing data. Several protocols are supported, please see the [usage documenation](https://nf-co.re/airrflow/usage) for more details on the supported protocols.
+nf-core/airrflow allows the end-to-end processing of BCR and TCR bulk and single cell targeted sequencing data. Several protocols are supported, please see the [usage documentation](https://nf-co.re/airrflow/usage) for more details on the supported protocols.
 
 ![nf-core/airrflow overview](docs/images/metro-map-airrflow.png)
 
@@ -77,10 +77,11 @@ nf-core/airrflow allows the end-to-end processing of BCR and TCR bulk and single
 
 ## Usage
 
-> **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.
+:::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.
+:::
 
 First, ensure that the pipeline tests run on your infrastructure:
 
@@ -124,16 +125,17 @@ nextflow run nf-core/airrflow \
 
 See the [usage documentation](https://nf-co.re/airrflow/usage) and the [parameter documentation](https://nf-co.re/airrflow/parameters) for more details on how to use the pipeline and all the available parameters.
 
-> **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).
+:::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 and further functionality, please refer to the [usage documentation](https://nf-co.re/airrflow/usage) and the [parameter documentation](https://nf-co.re/airrflow/parameters).
 
 ## Pipeline output
 
-To see the results of an example 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.
+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).
 

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/3.1.0" target="_blank">nf-core/airrflow</a>
+  This report has been generated by the <a href="https://nf-co.re/airrflow/3.2.0" 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/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -93,7 +93,6 @@ def check_samplesheet(file_in, assembled):
             "subject_id",
             "species",
             "pcr_target_locus",
-            "tissue",
         ]
 
         ## Read header

diff --git a/conf/modules.config b/conf/modules.config
@@ -510,4 +510,13 @@ process {
         ]
     }
 
+    withName: 'MULTIQC' {
+        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
 }
diff --git a/docs/output.md b/docs/output.md
@@ -212,7 +212,9 @@ Remove sequences which do not have 2 representative using [SplitSeq](https://pre
 
 ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
 
-> **NB:** Two sets of FastQC plots are displayed in the MultiQC report: first for the raw _untrimmed_ and unmated reads and secondly for the assembled and QC filtered reads (but before collapsing duplicates). They may contain adapter sequence and potentially regions with low quality.
+:::note
+Two sets of FastQC plots are displayed in the MultiQC report: first for the raw _untrimmed_ and unmated reads and secondly for the assembled and QC filtered reads (but before collapsing duplicates). They may contain adapter sequence and potentially regions with low quality.
+:::
 
 ## VDJ annotation
 
@@ -507,6 +509,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+  - Parameters used by the pipeline run: `params.json`.
 
 </details>
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -56,7 +56,9 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::warning
+Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -93,7 +95,9 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducibility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::tip
+If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::
 
 ## Input samplesheet
 
@@ -367,15 +371,19 @@ The UMI barcodes are typically read from an index file but sometimes can be prov
 
 ## Core Nextflow arguments
 
-> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::note
+These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::
 
 ### `-profile`
 
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::info
+We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::
 
 The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 

diff --git a/lib/WorkflowAirrflow.groovy b/lib/WorkflowAirrflow.groovy
@@ -46,7 +46,6 @@ class WorkflowAirrflow {
 
     public static String toolCitationText(params) {
 
-        // TODO Optionally add in-text citation tools to this list.
         // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
         // Uncomment function in methodsDescriptionText to render in MultiQC report
         def citation_text = [
@@ -61,7 +60,6 @@ class WorkflowAirrflow {
 
     public static String toolBibliographyText(params) {
 
-        // TODO Optionally add bibliographic entries to this list.
         // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
         // Uncomment function in methodsDescriptionText to render in MultiQC report
         def reference_text = [
@@ -86,7 +84,7 @@ class WorkflowAirrflow {
         meta["tool_citations"] = ""
         meta["tool_bibliography"] = ""
 
-        // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+        // Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
         //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
         //meta["tool_bibliography"] = toolBibliographyText(params)
 

diff --git a/modules.json b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {

diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf
@@ -6,8 +6,8 @@ process AIRRFLOW_REPORT {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     tuple val(meta), path(tab) // sequence tsv table in AIRR format

diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf
@@ -8,8 +8,8 @@ process COLLAPSE_DUPLICATES {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ]

diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf
@@ -25,8 +25,8 @@ process DEFINE_CLONES {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format

diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf
@@ -9,8 +9,8 @@ process DETECT_CONTAMINATION {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     path(tabs)

diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf
@@ -25,8 +25,8 @@ process DOWSER_LINEAGES {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     tuple val(meta), path(tabs)

diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf
@@ -25,8 +25,8 @@ process FIND_THRESHOLD {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
 
     input:

diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf
@@ -9,8 +9,8 @@ process REMOVE_CHIMERIC {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
 
     input:

diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf
@@ -10,8 +10,8 @@ process REPORT_FILE_SIZE {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     path logs

diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf
@@ -24,8 +24,8 @@ process SINGLE_CELL_QC {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     path(tabs)

diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf
@@ -10,8 +10,8 @@ process VALIDATE_INPUT {
         error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
     }
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/immcantation/airrflow:devel':
-        'docker.io/immcantation/airrflow:devel' }"
+        'docker.io/immcantation/airrflow:3.2.0':
+        'docker.io/immcantation/airrflow:3.2.0' }"
 
     input:
     file samplesheet