Merge pull request nf-core#94 from nf-core/dev

Release nf-core/pixelator 1.2.0
PixelgenTechnologies · May 28, 2024 · 35c594f · 35c594f
2 parents e0ab35d + 9bf3bf1
commit 35c594f
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diff --git a/.editorconfig b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/pixelator'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -30,7 +30,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/pixelator'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -28,10 +28,10 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,12 +1,8 @@
 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
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,6 +5,8 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - [email protected]
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"

diff --git a/.prettierignore b/.prettierignore
@@ -1,7 +1,6 @@
 email_template.html
 adaptivecard.json
 slackreport.json
-.devcontainer/devcontainer.json
 .nextflow*
 work/
 data/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,30 @@
 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).
 
+## [[1.2.0](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

diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/pixelator)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pixelator)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pixelator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pixelator)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 

diff --git a/conf/base.config b/conf/base.config
@@ -41,14 +41,14 @@ process {
     }
     withLabel:process_high {
         cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
+        memory = { check_max( 64.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 16.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_long {
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 128.GB * task.attempt, 'memory' ) }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
@@ -57,7 +57,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -46,13 +46,6 @@ process {
         publishDir = [ enabled: false ]
     }
 
-    withName: RENAME_READS {
-        publishDir = [
-            enabled: false,
-            path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        ]
-    }
-
 
     // use explicit (params.my_option instanceof Integer) checks to avoid issues with 0 evaluating false
     // since most pixelator flags do accept zero as a value
@@ -133,25 +126,25 @@ process {
             params.compute_polarization ? "--compute-polarization" : '',
             params.compute_colocalization ? "--compute-colocalization" : '',
             params.use_full_bipartite ? "--use-full-bipartite " : '',
-            params.polarization_normalization ? "--polarization-normalization ${params.polarization_normalization}" : '',
-            params.polarization_binarization ? "--polarization-binarization" : '',
+            params.polarization_min_marker_count ? "--polarization-min-marker-count ${params.polarization_min_marker_count}" : '',
+            params.polarization_transformation ? "--polarization-transformation ${params.polarization_transformation}" : '',
             params.colocalization_transformation ? "--colocalization-transformation ${params.colocalization_transformation}" : '',
+            params.polarization_n_permutations ? "--polarization-n-permutations ${params.polarization_n_permutations}" : '',
             (params.colocalization_neighbourhood_size instanceof Integer) ? "--colocalization-neighbourhood-size ${params.colocalization_neighbourhood_size}" : '',
             (params.colocalization_n_permutations instanceof Integer) ? "--colocalization-n-permutations ${params.colocalization_n_permutations}" : '',
             (params.colocalization_min_region_count instanceof Integer) ? "--colocalization-min-region-count ${params.colocalization_min_region_count}" : '',
         ].join(' ').trim()
     }
 
-    withName: PIXELATOR_REPORT {
-        ext.when = { !params.skip_report }
+    withName: PIXELATOR_LAYOUT {
+        ext.when = { !params.skip_layout }
+        ext.args = [
+            params.no_node_marker_counts ? "--no-node-marker-counts" : '',
+            params.layout_algorithm ? "--layout-algorithm ${params.layout_algorithm} " : '',
+        ].join(' ').trim()
     }
 
-
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
+    withName: PIXELATOR_REPORT {
+        ext.when = { !params.skip_report }
     }
 }
diff --git a/conf/test.config b/conf/test.config
@@ -23,8 +23,9 @@ params {
     max_memory = '6.GB'
     max_time   = '6.h'
 
-    input  = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/samplesheet/samplesheet.csv"
-    input_basedir  = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/testdata"
+    // Input data
+    input          = params.pipelines_testdata_base_path + 'pixelator/samplesheet/samplesheet.csv'
+    input_basedir  = params.pipelines_testdata_base_path + 'pixelator/testdata'
 
     multiplet_recovery = true
     min_size = 2
@@ -34,4 +35,10 @@ params {
     colocalization_min_region_count = 0
     colocalization_n_permutations = 10
     colocalization_neighbourhood_size = 1
+
+    // For now skip the layout step since it is very slow on these
+    // small test datasets
+    skip_layout = true
+    // using this since the default pmds_3d does not work on very small graphs
+    layout_algorithm = "fruchterman_reingold_3d"
 }