Merge pull request #3210 from nf-core/dev

mev -> main for 3.0.1

.github/workflows/pytest.yml

@@ -142,18 +142,18 @@ jobs:
             exit 1
           fi
 
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
       - name: Store snapshot report
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         if: always()
         with:
-          name: Snapshot Report ${{ matrix.test }}
+          name: Snapshot Report ${{ env.test }}
           path: ./snapshot_report.html
 
-      - name: remove slashes from test name
-        run: |
-          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
-          echo "test=${test}" >> $GITHUB_ENV
-
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:

CHANGELOG.md

@@ -1,5 +1,15 @@
 # nf-core/tools: Changelog
 
+## [v3.0.1 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.1) - [2024-10-09]
+
+### Template
+
+- Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202))
+- Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
+- Fix too many empty lines added by jinja ([#3204](https://github.com/nf-core/tools/pull/3204) and [#3206](https://github.com/nf-core/tools/pull/3206))
+- Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
+- Update included subworkflows and modules ([#3208](https://github.com/nf-core/tools/pull/3208))
+
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 
 **Highlights**

nf_core/modules/lint/main_nf.py

@@ -342,6 +342,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
             continue
         try:
             container_url = "https://" + urlunparse(url) if not url.scheme == "https" else urlunparse(url)
+            log.debug(f"Trying to connect to URL: {container_url}")
             response = requests.head(
                 container_url,
                 stream=True,

nf_core/pipeline-template/.editorconfig

@@ -11,7 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-{% if modules %}
+{% if modules -%}
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -25,12 +25,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-{% endif %}
+{%- endif %}
 
-{% if email %}
+{% if email -%}
 [/assets/email*]
 indent_size = unset
-{% endif %}
+{%- endif %}
 
 # ignore python and markdown
 [*.{py,md}]

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -30,7 +30,7 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-{%- if test_config %}
+{% if test_config -%}
 You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
 
 ```bash
@@ -139,4 +139,4 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-  {% endif %}
+  {%- endif %}

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -14,16 +14,18 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == '{{ name }}' && github.event.review.state == 'approved'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/request-action@v2.x
         id: check_approvals
         with:
-          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -42,10 +42,10 @@ jobs:
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
-          config: ${{ github.workspace }}/.nf-core.yaml
+          config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
         run: |

nf_core/pipeline-template/.prettierignore

@@ -1,4 +1,4 @@
-{%- if email %}
+{% if email -%}
 email_template.html
 {%- endif %}
 {%- if adaptivecard %}

nf_core/pipeline-template/docs/output.md

@@ -12,12 +12,16 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-{% if fastqc %}- [FastQC](#fastqc) - Raw read QC{% endif %}
-{% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
+{% if fastqc -%}
 
+- [FastQC](#fastqc) - Raw read QC
+  {%- endif %}
+  {%- if multiqc %}
+- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+  {%- endif %}
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-{%- if fastqc %}
+{% if fastqc -%}
 
 ### FastQC
 
@@ -32,7 +36,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 {%- endif %}
-{%- if multiqc %}
+
+{% if multiqc -%}
 
 ### MultiQC
 
@@ -49,7 +54,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
-{% endif %}
+{%- endif %}
 
 ### Pipeline information
 

nf_core/pipeline-template/modules.json

@@ -13,7 +13,7 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {

nf_core/pipeline-template/nextflow.config

@@ -13,14 +13,14 @@ params {
     // Input options
     input                      = null
 
-    {%- if igenomes %}
+    {% if igenomes -%}
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     {%- endif %}
 
-    {%- if multiqc %}
+    {% if multiqc -%}
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -45,7 +45,7 @@ params {
     version                      = false
     {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
-    {%- if nf_core_configs %}
+    {% if nf_core_configs -%}
     // Config options
     config_profile_name        = null
     config_profile_description = null
@@ -56,15 +56,17 @@ params {
     config_profile_url         = null
     {%- endif %}
 
-    {%- if nf_schema %}
+    {% if nf_schema -%}
     // Schema validation default options
     validate_params            = true
-    {% endif %}
+    {%- endif %}
 }
-{% if modules %}
+
+{% if modules -%}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 {%- else %}
+
 process {
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1    * task.attempt }
@@ -75,7 +77,7 @@ process {
     maxRetries    = 1
     maxErrors     = '-1'
 }
-{% endif %}
+{%- endif %}
 
 profiles {
     debug {
@@ -171,14 +173,14 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    {%- if gitpod %}
+    {% if gitpod -%}
     gitpod {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
     {%- endif %}
-    {%- if test_config %}
+    {% if test_config -%}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
     {%- endif %}
@@ -191,7 +193,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 // Load {{ name }} custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
-{% endif -%}
+{%- endif %}
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -205,7 +207,7 @@ charliecloud.registry = 'quay.io'
 {% if igenomes -%}
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
-{% endif -%}
+{%- endif %}
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
@@ -273,7 +275,7 @@ validation {
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-        {%- if is_nfcore %}
+        {% if is_nfcore -%}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -297,8 +299,9 @@ validation {
         afterText = validation.help.afterText
     }{% endif %}
 }
-{% endif -%}
-{%- if modules %}
+{%- endif %}
+
+{% if modules -%}
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-{% endif %}
+{%- endif %}