Merge branch 'dev' into nf-core-template-merge-3.1.0

nf-core · Dec 13, 2024 · dd40572 · dd40572
2 parents f36120b + 3b80478
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diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -45,9 +45,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

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/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: ${{ secrets.BSKY_PASSWORD }}
+          #
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+.idea
+.vscode
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,11 +1,12 @@
 lint:
+  multiqc_config: false
+  files_unchanged:
+    - assets/nf-core-pixelator_logo_light.png
   files_exist:
     - assets/multiqc_config.yml
     - conf/igenomes.config
-  files_unchanged:
-    - assets/nf-core-pixelator_logo_light.png
-  multiqc_config: false
 nf_core_version: 3.1.0
+org_path: null
 repository_type: pipeline
 template:
   author: Pixelgen Technologies AB
@@ -19,4 +20,4 @@ template:
     - fastqc
     - multiqc
     - igenomes
-  version: 1.3.1
+  version: 1.4.0
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,3 +1,5 @@
+exclude: ^(.*.test.snap)$
+
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.1.0"
@@ -11,3 +13,8 @@ repos:
     hooks:
       - id: editorconfig-checker
         alias: ec
+
+  - repo: https://github.com/psf/black
+    rev: 24.2.0
+    hooks:
+      - id: black
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,14 +3,158 @@
 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).
 
-## v1.3.1 - [date]
+## [[1.4.0dev](https://github.com/nf-core/pixelator/releases/tag/1.4.0] - ????-??-??
 
-Initial release of nf-core/pixelator, created with the [nf-core](https://nf-co.re/) template.
+### Enhancements & fixes
 
-### `Added`
+- [[PR #111](https://github.com/nf-core/pixelator/pull/111)] - Template update for nf-core/tools v3.0.2
+- [[PR #112](https://github.com/nf-core/pixelator/pull/112)] - Add graph refinement options for pixelator 0.19
+- [[PR #113](https://github.com/nf-core/pixelator/pull/113)] - Fix validation issues after nf-core/tools v3.0.2 update
+- [[PR #114](https://github.com/nf-core/pixelator/pull/114)] - Remove `--save_recovered_components` options for graph outputs
+- [[PR #115](https://github.com/nf-core/pixelator/pull/115)] - Update containers for pixelator 0.19
 
-### `Fixed`
+### Parameters
 
-### `Dependencies`
+| Old parameter                        | New parameter                            |
+| ------------------------------------ | ---------------------------------------- |
+|                                      | `--help_full`                            |
+|                                      | `--show_hidden`                          |
+| `--validationFailUnrecognisedParams` |                                          |
+| `--validationLenientMode`            |                                          |
+| `--validationSchemaIgnoreParams`     |                                          |
+| `--validationShowHiddenParams`       |                                          |
+| `--leiden_iterations`                | `--graph_max_refinement_recursion_depth` |
+|                                      | `--graph_max_edges_to_split`             |
+|                                      | `--graph_max_edges_to_split`             |
+| `--save_recovered_components`        |                                          |
 
-### `Deprecated`
+> [!NOTE]
+> Parameter has been **updated** if both old and new parameter information is present.
+> Parameter has been **added** if just the new parameter information is present.
+> Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.18.2      | 0.19.0      |
+
+> [!NOTE]
+> Dependency has been **updated** if both old and new parameter information is present.
+> Dependency has been **added** if just the new parameter information is present.
+> Dependency has been **removed** if new parameter information isn't present.
+
+## [[1.3.1](https://github.com/nf-core/pixelator/releases/tag/1.3.1)] - 2024-07-31
+
+### Enhancements & fixes
+
+- [[PR #107](https://github.com/nf-core/pixelator/pull/107)] - Fix conda version tag to use pixelator 0.18.2
+
+## [[1.3.0](https://github.com/nf-core/pixelator/releases/tag/1.3.0)] - 2024-07-17
+
+### Enhancements & fixes
+
+- [[PR #97](https://github.com/nf-core/pixelator/pull/97)] - Update citations
+- [[PR #96](https://github.com/nf-core/pixelator/pull/96)] - Make all ext.args assignments closures
+- [[PR #98](https://github.com/nf-core/pixelator/pull/98)] - Update metromap to include layout step
+- [[PR #99](https://github.com/nf-core/pixelator/pull/99)] - Update README to include layout step
+- [[PR #100](https://github.com/nf-core/pixelator/pull/100)] - Use R1/R2 suffixes in amplicon input fastq file renaming
+- [[PR #101](https://github.com/nf-core/pixelator/pull/101)] - Fix validation issue when using panel_file instead of panel
+- [[PR #102](https://github.com/nf-core/pixelator/pull/101)] - Restructure output directory
+- [[PR #103](https://github.com/nf-core/pixelator/pull/103)] - Make rate-diff the default transformation method when computing colocalization
+- [[PR #104](https://github.com/nf-core/pixelator/pull/104)] - Update to pixelator 0.18.1
+- [[PR #106](https://github.com/nf-core/pixelator/pull/106)] - Update to pixelator 0.18.2
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.17.1      | 0.18.2      |
+
+> [!NOTE]
+> Dependency has been **updated** if both old and new version information is present.
+> Dependency has been **added** if just the new version information is present.
+> Dependency has been **removed** if new version information isn't present.
+
+## [[1.2.0](https://github.com/nf-core/pixelator/releases/tag/1.2.0)] - 2024-05-28
+
+### Enhancements & fixes
+
+- [[PR #89](https://github.com/nf-core/pixelator/pull/89)] - Template update for nf-core/tools v2.14.1
+- [[PR #90](https://github.com/nf-core/pixelator/pull/90)] - Update pixelator to 0.17.1
+- [[PR #90](https://github.com/nf-core/pixelator/pull/90)] - Add `pixelator single-cell layout` command
+- [[PR #90](https://github.com/nf-core/pixelator/pull/90)] - The `graph` and `annotate` steps are now using `process_high` as their resource tags
+- [[PR #91](https://github.com/nf-core/pixelator/pull/91)] - Set `process_high` to use 64GB of RAM and `process_high_memory` to use 128GB of RAM
+- [[PR #92](https://github.com/nf-core/pixelator/pull/92)] - Minor touch-ups to the documentation
+- [[PR #93](https://github.com/nf-core/pixelator/pull/93)] - Merge RENAME_READS functionality into PIXELATOR_AMPLICON
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.16.2      | 0.17.1      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
+## [[1.1.0](https://github.com/nf-core/pixelator/releases/tag/1.1.0)] - 2024-03-29
+
+### Enhancements & fixes
+
+- [[PR #83](https://github.com/nf-core/pixelator/pull/83)] - Template update for nf-core/tools v2.13
+- [[PR #84](https://github.com/nf-core/pixelator/pull/84)] - Update pixelator to 0.16.2, collapse`and`graph` step now return parquet files
+- [[PR #85](https://github.com/nf-core/pixelator/pull/85)] - Remove a workaround for container issues, silence some warnings, update default resources
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.15.2      | 0.16.2      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
+## [[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](https://github.com/nf-core/pixelator/releases/tag/1.0.1)] - 2023-10-27
+
+### Enhancements & fixes
+
+- [[PR #66](https://github.com/nf-core/pixelator/pull/66)] - Add a warning and workaround for singularity & apptainer
+- Cleanup some linting warnings
+- Update docker image in RENAME_READS to match the singularity container
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.15.0      | 0.15.2      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
+## [[1.0.0](https://github.com/nf-core/pixelator/releases/tag/1.0.0)] - 2023-10-17
+
+Initial release of nf-core/pixelator.
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -10,6 +10,18 @@
 
 ## Pipeline tools
 
+- [pixelator](https://doi.org/10.1038/s41592-024-02268-9)
+
+  > Karlsson, F., Kallas, T., Thiagarajan, D. et al. “Molecular pixelation: spatial proteomics of single cells by sequencing.“ Nat Methods 21, 1044–1052 (2024). https://doi.org/10.1038/s41592-024-02268-9
+
+- [cutadapt](http://dx.doi.org/10.14806/ej.17.1.200)
+
+  > Martin, Marcel. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.Journal 17, no. 1 (May 2, 2011): 10–12. https://doi.org/10.14806/ej.17.1.200.
+
+- [fastp](https://doi.org/10.1002/imt2.107)
+
+  > Chen, Shifu. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” IMeta 2, no. 2 (2023): e107. https://doi.org/10.1002/imt2.107.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,3 +7,5 @@ testing/ @@
     testing*
     *.pyc
     null/
+    .idea
+    .vscode