Important! Template update for nf-core/tools v3.0.2

.github/workflows/ci.yml

@@ -16,6 +16,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   NFTEST_VER: "0.9.0"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
@@ -27,31 +29,68 @@ concurrency:
 
 jobs:
   test:
-    name: Run nf-test with standard profiles
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/phaseimpute') }}"
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "24.04.4"
+          - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
         TEST_PROFILE:
           - "test_all"
           - "test_validate"
           - "test_stitch"
           - "test_dog"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
+
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Install pdiff to see diff between nf-test snapshots
@@ -64,16 +103,6 @@ jobs:
           wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
           sudo mv nf-test /usr/local/bin/
 
-      - name: Run pipeline with test data
-        run: |
-          nf-test test --tag "${{ matrix.TEST_PROFILE }}" --profile docker --verbose
-
-      - name: Run pipeline with test data (singularity)
-        run: |
-          nf-test test --tag "${{ matrix.TEST_PROFILE }}" --profile singularity
-        if: "${{ github.base_ref == 'master' }}"
-
-      - name: Run pipeline with test data (conda)
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nf-test test --tag "${{ matrix.TEST_PROFILE }}" --profile conda
-        if: "${{ github.base_ref == 'master' }}"
+          nf-test test --tag "${{ matrix.TEST_PROFILE }}" --profile ${{ matrix.profile }} --verbose

.github/workflows/template_version_comment.yml

@@ -1,6 +1,6 @@
 name: nf-core template version comment
 # This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
-# It posts a comment to the PR, even if it comes from a fork.{%- raw %}
+# It posts a comment to the PR, even if it comes from a fork.
 
 on: pull_request_target
 
@@ -14,7 +14,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -26,12 +26,12 @@ jobs:
 
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          contains(steps.nf_core_outdated.outputs.stdout, 'nf-core')
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
@@ -43,4 +43,4 @@ jobs:
             > Please update your pipeline to the latest version.
             >
             > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
-          #{%- endraw %}
+          #

.gitignore

@@ -6,6 +6,7 @@ results/
 testing/
 testing*
 *.pyc
+null/
 *.code-workspace
 .nf-test*
 *.xml.bkp

.nf-core.yml

@@ -1,7 +1,7 @@
 bump_version: null
 lint:
   subworkflow_changes: false
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) LouisLeNezet
+Copyright (c) Louis Le Nezet, Anabella Trigila
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -10,7 +10,7 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/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)
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.4-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.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/)
 [![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/)
@@ -95,11 +95,10 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/phaseimpute was originally written by Louis Le Nézet.
+nf-core/phaseimpute was originally written by Louis Le Nézet & Anabella Trigila.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-- Anabella Trigila
 - Saul Pierotti
 - Eugenia Fontecha
 - Matias Romero Victorica

docs/usage.md

@@ -563,14 +563,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-## Azure Resource Requests
-
-To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
-
-Note that the choice of VM size depends on your quota and the overall workload during the analysis.
-For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
-
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.

main.nf

@@ -103,7 +103,6 @@ workflow NFCORE_PHASEIMPUTE {
         ch_chunks,
         ch_versions
     )
-
     emit:
     multiqc_report = PHASEIMPUTE.out.multiqc_report // channel: /path/to/multiqc_report.html
 }

modules.json

@@ -124,7 +124,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "quilt/quilt": {

modules/local/add_columns/environment.yml

@@ -2,6 +2,5 @@ name: gawk
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - anaconda::gawk=5.3.0

nextflow.config

@@ -271,11 +271,11 @@ dag {
 
 manifest {
     name            = 'nf-core/phaseimpute'
-    author          = """LouisLeNezet"""
+    author          = """Louis Le Nezet, Anabella Trigila"""
     homePage        = 'https://github.com/nf-core/phaseimpute'
     description     = """Phasing and imputation pipeline"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=24.04.4'
+    nextflowVersion = '!>=24.04.2'
     version         = '1.0dev'
     doi             = ''
 }

subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf

@@ -66,6 +66,7 @@ workflow PIPELINE_INITIALISATION {
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
+
     //
     // Custom validation for pipeline parameters
     //