Merge pull request #79 from nf-core/dev

Release 1.0.3

.github/CONTRIBUTING.md

@@ -27,6 +27,9 @@ 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>`.
+
 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.
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pixe
 - [ ] If necessary, also make a PR on the nf-core/pixelator _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>`).
+- [ ] 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.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/ci.yml

@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

.github/workflows/linting.yml

@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/release-announcements.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/bluesky-post-action@v0.0.2
+        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

@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

.nf-core.yml

@@ -7,3 +7,4 @@ lint:
     - conf/igenomes.config
   files_unchanged:
     - lib/NfcoreTemplate.groovy
+    - .prettierignore

.prettierignore

@@ -1,6 +1,7 @@
 email_template.html
 adaptivecard.json
 slackreport.json
+.devcontainer/devcontainer.json
 .nextflow*
 work/
 data/

CHANGELOG.md

@@ -3,13 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.0.2] - 2023-11-20
+## [[1.0.3](https://github.com/nf-core/pixelator/releases/tag/1.0.3)] - 2024-01-19
+
+### Enhancements & fixes
+
+- [[PR #74](https://github.com/nf-core/pixelator/pull/74)] - Template update for nf-core/tools v2.11
+- [[e196431](https://github.com/nf-core/pixelator/commit/e196431842b039cbf5c299c7a3e568f6a3e30e33)] - Workaround a tool issue by removing `docker.runOptions` user and group flags
+- [[PR #76](https://github.com/nf-core/pixelator/pull/76)] - Use `adapterqc` output as main output of PIXELATOR_QC
+- [[PR #77](https://github.com/nf-core/pixelator/pull/77)] - Fix some style issues in nextflow_schema.json
+
+## [[1.0.2](https://github.com/nf-core/pixelator/releases/tag/1.0.2)] - 2023-11-20
 
 ### Enhancements & fixes
 
 - [[PR #70](https://github.com/nf-core/pixelator/pull/70)] - Fix loading of absolute paths and urls in input samplesheet
 
-## [1.0.1] - 2023-10-27
+## [[1.0.1](https://github.com/nf-core/pixelator/releases/tag/1.0.1)] - 2023-10-27
 
 ### Enhancements & fixes
 
@@ -29,6 +38,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 >
 > **NB:** Dependency has been **removed** if new version information isn't present.
 
-## [1.0.0] - 2023-10-17
+## [[1.0.0](https://github.com/nf-core/pixelator/releases/tag/1.0.0)] - 2023-10-17
 
 Initial release of nf-core/pixelator.

README.md

@@ -27,18 +27,15 @@ It takes a samplesheet as input and will process your data using `pixelator` to
 7. Analyze the cells for polarization and colocalization ([`pixelator analysis`](https://github.com/PixelgenTechnologies/pixelator))
 8. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))
 
-> **Warning**
+> [!WARNING]
 > Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
 > This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable
 > `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.
 
 ## 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, prepare a samplesheet with your input data that looks as follows:
 
@@ -60,11 +57,9 @@ nextflow run nf-core/pixelator \
    --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/pixelator/usage) and the [parameter documentation](https://nf-co.re/pixelator/parameters).
 

assets/nf-params.yml

@@ -1,5 +1,5 @@
 ## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-##     nf-core/pixelator 1.0.1
+##     nf-core/pixelator 1.0.3
 ## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ##     This is an example parameter file to pass to the `-params-file` option
 ##     of nextflow run with the nf-core/pixelator pipeline.
@@ -107,15 +107,15 @@
 ##     Remove duplicated reads (exact same sequence)
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# dedup = false
+# dedup = null
 
 ## -----------------------------------------------------------------------------
 ## remove_polyg
 ## -----------------------------------------------------------------------------
 ##     Remove PolyG sequences (length of 10 or more)
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# remove_polyg = false
+# remove_polyg = null
 
 
 ## =============================================================================
@@ -171,7 +171,7 @@
 ## -----------------------------------------------------------------------------
 ## algorithm
 ## -----------------------------------------------------------------------------
-##     The algorithm to use for collapsing (adjacency will peform error
+##     The algorithm to use for collapsing (adjacency will perform error
 ##     correction using the number of mismatches given)
 ##     Type: string
 ## -----------------------------------------------------------------------------
@@ -271,7 +271,7 @@
 ##     Skip analysis step
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# skip_analysis = false
+# skip_analysis = null
 
 ## -----------------------------------------------------------------------------
 ## compute_polarization
@@ -296,7 +296,7 @@
 ##     computing polarization, coabundance and colocalization scores
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# use_full_bipartite = false
+# use_full_bipartite = null
 
 ## -----------------------------------------------------------------------------
 ## polarization_normalization
@@ -313,7 +313,7 @@
 ##     polarization
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# polarization_binarization = false
+# polarization_binarization = null
 
 ## -----------------------------------------------------------------------------
 ## colocalization_transformation
@@ -345,7 +345,7 @@
 ## -----------------------------------------------------------------------------
 ## colocalization_min_region_count
 ## -----------------------------------------------------------------------------
-##     The minimum number of counts in a region for it to be concidered valid
+##     The minimum number of counts in a region for it to be considered valid
 ##     for computing colocalization
 ##     Type: integer
 ## -----------------------------------------------------------------------------
@@ -362,7 +362,7 @@
 ##     Skip report generation
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# skip_report = false
+# skip_report = null
 
 
 ## =============================================================================

docs/usage.md

@@ -54,7 +54,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end based on
 
 The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
 
-```csv
+```csv title="samplesheet.csv"
 sample,design,panel,fastq_1,fastq_2
 uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L001_R1_001.fastq.gz,uropod_control_S1_L001_R2_001.fastq.gz
 uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L002_R1_001.fastq.gz,uropod_control_S1_L002_R2_001.fastq.gz
@@ -78,7 +78,7 @@ Given following directory structure:
 
 You can use following samplesheet:
 
-```csv
+```csv title="samplesheet.csv"
 sample,design,panel,panel_file,fastq_1,fastq_2
 sample1,D21,human-sc-immunology-spatial-proteomics,,fastq/sample1_R1.fq.gz,fastq/sample1_R2.fq.gz
 ```

lib/NfcoreTemplate.groovy

@@ -142,6 +142,8 @@ class NfcoreTemplate {
             try {
                 if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
                 // Try to send HTML e-mail using sendmail
+                def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+                sendmail_tf.withWriter { w -> w << sendmail_html }
                 [ 'sendmail', '-t' ].execute() << sendmail_html
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
             } catch (all) {

modules.json

@@ -7,12 +7,12 @@
                 "nf-core": {
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     }
                 }

modules/local/pixelator/single-cell/qc/main.nf

@@ -12,7 +12,7 @@ process PIXELATOR_QC {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("preqc/*.processed.{fq,fastq}.gz")         , emit: processed
+    tuple val(meta), path("adapterqc/*.processed.{fq,fastq}.gz")     , emit: processed
 
     tuple val(meta), path("adapterqc/*.processed.{fq,fastq}.gz")     , emit: adapterqc_processed
     tuple val(meta), path("preqc/*.processed.{fq,fastq}.gz")         , emit: preqc_processed