Update nf-core template v2.10

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

.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 }}
+          #

CITATIONS.md

@@ -12,6 +12,8 @@
 
 - [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://github.com/OpenGene/fastp)
 
   > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PMID: 30423086; PMCID: PMC6129281.

README.md

@@ -42,10 +42,11 @@ In all cases, the assembly is assessed using [QUAST](http://bioinf.spbau.ru/quas
 
 ## 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.
+:::
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):-->
@@ -85,10 +86,11 @@ nextflow run nf-core/bacass \
    --outdir <OUTDIR>
 ```
 
-> **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/bacass/usage) and the [parameter documentation](https://nf-co.re/bacass/parameters).
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/bacass/2.1.0dev" target="_blank">nf-core/bacass</a>
+  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/dev" target="_blank">nf-core/bacass</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/bacass/2.1.0dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/bacass/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-bacass-methods-description":
     order: -1000

docs/output.md

@@ -42,7 +42,15 @@ combines reads coming from multiple sequencing runs.
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
+
+![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
+
+![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
+
+:::note
+The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -233,5 +241,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 - `pipeline_info/`
   - 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>

docs/usage.md

@@ -61,7 +61,9 @@ 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:
 
@@ -97,19 +99,25 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducbility, 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.
+:::
 
 ## 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).
 

lib/NfcoreTemplate.groovy

@@ -3,6 +3,7 @@
 //
 
 import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
 
 class NfcoreTemplate {
 
@@ -222,6 +223,21 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Dump pipeline parameters in a json file
+    //
+    public static void dump_parameters(workflow, params) {
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+
+        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def jsonStr    = JsonOutput.toJson(params)
+        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    }
+
     //
     // Print pipeline summary on completion
     //

lib/WorkflowBacass.groovy

@@ -49,7 +49,7 @@ class WorkflowBacass {
 
     public static String toolCitationText(params) {
 
-        // TODO Optionally add in-text citation tools to this list.
+        // TODO nf-core: 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 = [

nextflow.config

@@ -179,6 +179,7 @@ profiles {
     }
     apptainer {
         apptainer.enabled      = true
+        apptainer.autoMounts   = true
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -188,8 +189,8 @@ profiles {
     }
     gitpod {
         executor.name          = 'local'
-        executor.cpus          = 16
-        executor.memory        = 60.GB
+        executor.cpus          = 4
+        executor.memory        = 8.GB
     }
     test              { includeConfig 'conf/test.config'              }
     test_dfast        { includeConfig 'conf/test_dfast.config'        }

workflows/bacass.nf

@@ -448,6 +448,7 @@ workflow.onComplete {
     if (params.email || params.email_on_fail) {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
     }
+    NfcoreTemplate.dump_parameters(workflow, params)
     NfcoreTemplate.summary(workflow, params, log)
     if (params.hook_url) {
         NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)