Merge branch 'dev' into nf-core-template-merge-2.14.1

.github/workflows/awsfulltest.yml

@@ -15,9 +15,6 @@ jobs:
     steps:
       - 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 }}

.github/workflows/ci.yml

@@ -39,8 +39,5 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

.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 }}
+          #

.gitignore

@@ -6,3 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+.idea
+.vscode

.nf-core.yml

@@ -1,2 +1,13 @@
 repository_type: pipeline
 nf_core_version: "2.14.1"
+lint:
+  # No multiqc support for now
+  multiqc_config: false
+  files_exist:
+    - assets/multiqc_config.yml
+    - conf/igenomes.config
+  files_unchanged:
+    - lib/NfcoreTemplate.groovy
+    - .prettierignore
+    # Skip warning for a removed a reference to nf-test
+    - .github/PULL_REQUEST_TEMPLATE.md

.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

.prettierignore

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

CHANGELOG.md

@@ -3,14 +3,67 @@
 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).
 
-## v1.1.0 - [date]
+## [[1.2.0](https://github.com/nf-core/pixelator/releases/tag/1.2.0)] - UNRELEASED
 
-Initial release of nf-core/pixelator, created with the [nf-core](https://nf-co.re/) template.
+### Enhancements & fixes
 
-### `Added`
+- [[PR #89](https://github.com/nf-core/pixelator/pull/89)] - Template update for nf-core/tools v2.14.1
 
-### `Fixed`
+## [[1.1.0](https://github.com/nf-core/pixelator/releases/tag/1.1.0)] - 2024-03-29
 
-### `Dependencies`
+### Enhancements & fixes
 
-### `Deprecated`
+- [[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.

CITATIONS.md

@@ -10,13 +10,17 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [pixelator](https://doi.org/10.1101/2023.06.05.543770)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+  > Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+- [cutadapt](http://dx.doi.org/10.14806/ej.17.1.200)
 
-  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+  > 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
 

README.md

@@ -5,9 +5,8 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
-[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
+[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/pixelator/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/pixelator/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -19,46 +18,43 @@
 
 ## Introduction
 
-**nf-core/pixelator** is a bioinformatics pipeline that ...
+**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of Molecular Pixelation assays.
+It takes a samplesheet as input and will process your data using `pixelator` to produce final antibody counts.
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
+![](./docs/images/nf-core-pixelator-metromap.svg)
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+1. Build amplicon from input reads ([`pixelator amplicon`](https://github.com/PixelgenTechnologies/pixelator))
+2. Read QC and filtering, correctness of the pixel binding sequence sequences ([`pixelator preqc | pixelator adapterqc`](https://github.com/PixelgenTechnologies/pixelator))
+3. Assign a marker (barcode) to each read ([`pixelator demux`](https://github.com/PixelgenTechnologies/pixelator))
+4. Error correction, duplicate removal, compute read counts ([`pixelator collapse`](https://github.com/PixelgenTechnologies/pixelator))
+5. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator graph`](https://github.com/PixelgenTechnologies/pixelator))
+6. Call and annotate cells ([`pixelator annotate`](https://github.com/PixelgenTechnologies/pixelator))
+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))
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+> [!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.
 
-<!-- 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):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,design,panel,fastq_1,fastq_2
+uropod_control,D21,human-sc-immunology-spatial-proteomics,uropod_control_300k_S1_R1_001.fastq.gz,uropod_control_300k_S1_R2_001.fastq.gz
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
+Each row represents a sample and gives the design, a panel file and the input fastq files.
 
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/pixelator \
    -profile <docker/singularity/.../institute> \
@@ -80,11 +76,11 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/pixelator was originally written by Pixelgen Technologies AB.
-
-We thank the following people for their extensive assistance in the development of this pipeline:
+nf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- Florian De Temmerman
+- Johan Dahlberg
+- Alvaro Martinez Barrio
 
 ## Contributions and Support
 
@@ -94,10 +90,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+If you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.