Update to latest best practices

.editorconfig

@@ -28,7 +28,7 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-[/assets/haplotype maps/*]
+[/assets/haplotype_maps/*]
 charset = unset
 end_of_line = unset
 insert_final_newline = unset

.github/CONTRIBUTING.md

@@ -16,7 +16,7 @@ If you'd like to write some code for nf-cmgg/sampletracking, the standard workfl
 1. Check that there isn't already an issue about your idea in the [nf-cmgg/sampletracking issues](https://github.com/nf-cmgg/sampletracking/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-cmgg/sampletracking repository](https://github.com/nf-cmgg/sampletracking) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -37,7 +37,7 @@ There are typically two types of tests that run:
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -68,7 +68,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
@@ -79,11 +79,11 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -96,7 +96,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,46 +9,34 @@ body:
       description: A clear and concise description of what the bug is.
     validations:
       required: true
+
   - type: textarea
     id: command_used
     attributes:
       label: Command used and terminal output
-      description: Steps to reproduce the behaviour. Please paste the command you used
-        to launch the pipeline and the output from your terminal.
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
       render: console
-      placeholder: "$ nextflow run ...
-
+      placeholder: |
+        $ nextflow run ...
 
         Some output where something broke
 
-        "
   - type: textarea
     id: files
     attributes:
       label: Relevant files
-      description: "Please drag and drop the relevant files here. Create a `.zip` archive
-        if the extension is not allowed.
-
-        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-        in the directory where you launched the pipeline)_ as well as custom Nextflow
-        configuration files.
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
 
-        "
   - type: textarea
     id: system
     attributes:
       label: System information
-      description: "* Nextflow version _(eg. 23.04.0)_
-
+      description: |
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
-
         * Executor _(eg. slurm, local, awsbatch)_
-
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
-        or Apptainer)_
-
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
         * Version of nf-cmgg/sampletracking _(eg. 1.1, 1.5, 1.8.2)_
-
-        "

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,8 +16,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/samp
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/sampletracking/tree/master/.github/CONTRIBUTING.md)
-- [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/ci.yml

@@ -30,19 +30,17 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.1"
           - "latest-everything"
         tags:
           - "workflows"
           - "pipeline"
-        profile:
-          - "test,docker"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -76,7 +74,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose --tag ${{ matrix.tags }} --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:

.github/workflows/download_pipeline.yml

@@ -28,7 +28,7 @@ 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
         with:

.github/workflows/linting.yml

@@ -35,7 +35,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:

.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@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.gitignore

@@ -8,3 +8,4 @@ testing*
 *.pyc
 .env
 .nf-test*
+null

.nf-core.yml

@@ -13,6 +13,7 @@ lint:
     - docs/images/nf-core-sampletracking_logo_light.png
     - docs/images/nf-core-sampletracking_logo_dark.png
     - .github/workflows/linting.yml
+    - .gitignore
   multiqc_config:
     - report_comment
   nextflow_config:

README.md

@@ -4,7 +4,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-cmgg/sampletracking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/sampletracking/actions/workflows/linting.yml)[![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%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.1-23aa62.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/)

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-cmgg/sampletracking/master/assets/schema_input.json",
     "title": "nf-cmgg/sampletracking pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -11,8 +11,7 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id", "samplename"],
-                "unique": true
+                "meta": ["id", "samplename"]
             },
             "pool": {
                 "type": "string",
@@ -60,6 +59,7 @@
                 "errorMessage": "snp BAM/CRAM index file must be provided, cannot contain spaces and must have extension '.bai' or '.csi'"
             }
         },
+        "uniqueEntries": ["sample"],
         "anyOf": [
             {
                 "required": ["sample", "sample_bam", "snp_fastq_1", "snp_fastq_2"]

conf/base.config

@@ -10,47 +10,40 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 8.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
-    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
-    //        If possible, it would be nice to keep the same label naming convention when
-    //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 8.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 16.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 4     * task.attempt }
+        memory = { 32.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 8     * task.attempt }
+        memory = { 64.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
@@ -59,7 +52,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }

conf/empty_genomes.config

@@ -0,0 +1,3 @@
+// DON'T REMOVE THIS FILE!
+
+params.genomes = [:]

conf/test.config

@@ -14,17 +14,13 @@ params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     input = "${projectDir}/assets/samplesheet.csv"
     bwa_index = "s3://test-data/genomics/homo_sapiens/genome/bwa/"
     fasta   = "https://github.com/nf-cmgg/test-datasets/raw/sampletracking/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna"
     fai    = "https://github.com/nf-cmgg/test-datasets/raw/sampletracking/data/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai"
     haplotype_map = "https://github.com/nf-cmgg/test-datasets/raw/sampletracking/data/genomics/homo_sapiens/genome/picard/haplotype_map.txt"
 }
+
 aws {
     client {
         endpoint = "https://s3.ugent.be"
@@ -34,3 +30,12 @@ aws {
     }
 }
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus  : 2,
+        memory: 6.GB,
+        time  : 6.h
+    ]
+}
+