Merge pull request #124 from healx/merging-template-updates

Template update for nf-core/tools v2.8

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -45,6 +45,6 @@ body:
         * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/differentialabundance _(eg. 1.1, 1.5, 1.8.2)_

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/diff
 
 - [ ] 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-core/differentialabundance/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/differentialabundance _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/differentialabundance/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/differentialabundance _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/awsfulltest.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v1
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/awstest.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v1
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/differentialabundance'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/differentialabundance ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/differentialabundance ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/clean-up.yml

@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier

CHANGELOG.md

@@ -3,13 +3,15 @@
 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).
 
-## v1.3.0 - xxxx-xx-xx
+## v1.3.0dev - [date]
 
 ### `Added`
 
+- [[#124](https://github.com/nf-core/differentialabundance/pull/124)] - Template update for nf-core/tools v2.8 ([@pinin4fjords](https://github.com/pinin4fjords), review by )
+
 ### `Fixed`
 
-- [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by )
+- [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by [@nvnieuwk](https://github.com/nvnieuwk))
 
 ## v1.2.0 - 2023-04-19
 

README.md

@@ -8,7 +8,7 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/differentialabundance)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23differentialabundance-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/differentialabundance)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/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)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23differentialabundance-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/differentialabundance)[![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)
 
 ## Introduction
 
@@ -30,26 +30,12 @@ On release, automated continuous integration tests run the pipeline on a full-si
 6. Optionally build and (if specified) deploy a Shiny app for fully interactive mining of results.
 7. Build an HTML report based on R markdown, with interactive plots (where possible) and tables.
 
-## Quick Start
+## Usage
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
-
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
-
-3. Download the pipeline and test it on a minimal dataset with a single command:
-
-   ```bash
-   nextflow run nf-core/differentialabundance -profile test,YOURPROFILE --outdir <OUTDIR>
-   ```
-
-   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
-
-   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
-   > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
-   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
-
-4. Start running your own analysis!
+> **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.
 
 RNA-seq:
 
@@ -74,6 +60,13 @@ Affymetrix microarray:
      -profile affy,<docker/singularity/podman/shifter/charliecloud/conda/institute>
 ```
 
+> **Warning:**
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+
+For more details, please refer to the [usage documentation](https://nf-co.re/differentialabundance/usage) and the [parameter documentation](https://nf-co.re/differentialabundance/parameters).
+
 ### Reporting
 
 The pipeline reports its outcomes in two forms.
@@ -94,9 +87,11 @@ A second optional output is produced by leveraging [shinyngs](https://github.com
 
 By default the application is provided as an R script and associated serialised data structure, which you can use to quickly start the application locally. With proper configuration the app can also be deployed to [shinyapps.io](https://www.shinyapps.io/) - though this requires you to have an account on that service (free tier available).
 
-## Documentation
+## Pipeline output
 
-The nf-core/differentialabundance pipeline comes with documentation about the pipeline [usage](https://nf-co.re/differentialabundance/usage), [parameters](https://nf-co.re/differentialabundance/parameters) and [output](https://nf-co.re/differentialabundance/output).
+To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/differentialabundance/results) tab on the nf-core website pipeline page.
+For more details about the output files and reports, please refer to the
+[output documentation](https://nf-co.re/differentialabundance/output).
 
 ## Credits
 

bin/check_samplesheet.py

@@ -158,9 +158,6 @@ def sniff_format(handle):
     peek = read_head(handle)
     handle.seek(0)
     sniffer = csv.Sniffer()
-    if not sniffer.has_header(peek):
-        logger.critical("The given sample sheet does not appear to contain a header.")
-        sys.exit(1)
     dialect = sniffer.sniff(peek)
     return dialect
 

conf/base.config

@@ -14,7 +14,7 @@ process {
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
-    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 

conf/igenomes.config

@@ -36,6 +36,14 @@ params {
             macs_gsize  = "2.7e9"
             blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
         }
+        'CHM13' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
+            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
+            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
+            mito_name   = "chrM"
+        }
         'GRCm38' {
             fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
             bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"

conf/test_full.config

@@ -10,6 +10,8 @@
 ----------------------------------------------------------------------------------------
 */
 
+cleanup = true
+
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'