nf-core · chris-cheshire · Jan 20, 2022 · Oct 21, 2021 · Oct 21, 2021 · Oct 21, 2021
diff --git a/.gitattributes b/.gitattributes
@@ -1 +1,3 @@
 *.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -68,16 +68,13 @@ If you wish to contribute a new step, please use the following coding standards:
 1. Define the corresponding input channel into your new process from the expected previous process channel
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
-4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
-6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
-7. Add sanity checks for all relevant parameters.
-8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
-9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yml`.
-11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+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).
+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`.
+9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 
@@ -102,27 +99,6 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 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]`
 
-### Software version reporting
-
-If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
-
-Add to the script block of the process, something like the following:
-
-```bash
-<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-or
-
-```bash
-<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-You then need to edit the script `bin/scrape_software_versions.py` to:
-
-1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
-2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
-
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,52 @@
+
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/cutandrun pipeline documentation](https://nf-co.re/cutandrun/usage)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      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.
+      render: console
+      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.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/cutandrun _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,4 +1,3 @@
-blank_issues_enabled: false
 contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join

diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the nf-core/cutandrun pipeline
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -14,14 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@master
+        uses: nf-core/tower-action@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           pipeline: ${{ github.repository }}
           revision: ${{ github.sha }}
@@ -30,5 +30,5 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"
             }
-          profiles: '[ "test_full", "aws_tower" ]'
-
+          profiles: test_full,aws_tower
+          pre_run_script: 'export NXF_VER=21.10.3'
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -11,18 +11,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@master
+        uses: nf-core/tower-action@v2
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           pipeline: ${{ github.repository }}
           revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/cutandrun/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-test-${{ github.sha }}"
             }
-          profiles: '[ "test", "aws_tower" ]'
-
+          profiles: test,aws_tower
+          pre_run_script: 'export NXF_VER=21.10.3'
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,10 +20,15 @@ jobs:
     env:
       NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
+      CAPSULE_LOG: none
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.04.0', '']
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+          # Test latest nextflow version
+          - NXF_VER: ''
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -59,10 +64,11 @@ jobs:
     env:
       NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
+      CAPSULE_LOG: none
     strategy:
       matrix:
-        # We only run this on the specified nextflow version for the pipeline
-        nxf_ver: ['21.04.0']
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['21.10.3', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -99,6 +105,7 @@ jobs:
       NXF_VER: ''
       NXF_EDGE: 1
       NXF_ANSI_LOG: false
+      CAPSULE_LOG: none
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -133,10 +140,11 @@ jobs:
     runs-on: ubuntu-20.04
     env:
       NXF_ANSI_LOG: false
+      CAPSULE_LOG: none
     strategy:
       fail-fast: false
       matrix:
-        nxf_version: ["21.04.0"]
+        nxf_version: ['21.10.3', '']
         tags: ["samplesheet", "verify_output_input", "verify_output_align_short", "verify_output_align_long", "verify_output_peak_calling", "verify_output_reporting", "verify_output_save", "verify_output_skip"]
     steps:
       - uses: actions/checkout@v2

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -15,6 +15,7 @@ jobs:
         uses: dawidd6/action-download-artifact@v2
         with:
           workflow: linting.yml
+          workflow_conclusion: completed
 
       - name: Get PR number
         id: pr_number

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,3 +33,30 @@ We thank Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and everyone i
     2. Heatmap peak analysis ([`deepTools`](https://github.com/deeptools/deepTools/))
 13. Genome browser session ([`IGV`](https://software.broadinstitute.org/software/igv/))
 14. Present QC for raw read, alignment and duplicate reads ([`MultiQC`](http://multiqc.info/))
+
+## [1.1] - 2022-01-05
+
+### Enhancements & fixes
+
+* Updated pipeline template to nf-core/tools `2.2`
+* [[#71](https://github.com/nf-core/cutandrun/issues/71)] - Bumped Nextflow version `21.04.0` -> `21.10.3`
+* Added pipeline diagram to [[README](https://github.com/nf-core/cutandrun/blob/master/README.md)]
+* Upgraded all modules (local and nf-core) to support the new versioning system
+* The module `getchromsizes` was submitted to nf-core and moved from `local` to `nf-core`
+* Added support for GFF files in IGV session generation
+* [[#57](https://github.com/nf-core/cutandrun/issues/57), [#66](https://github.com/nf-core/cutandrun/issues/66)] - Upgraded version reporting in multiqc to support both software version by module and unique software versions. This improves detection of multi-version software usage in the pipeline
+* [[#54](https://github.com/nf-core/cutandrun/issues/54)] - Fixed pipeline error where dots in sample ids inside the sample sheet were not correctly handled
+* [[#75](https://github.com/nf-core/cutandrun/issues/75)] - Fixed error caused by emtpy peak files being passed to the `CALCULATE_FRIP` and `CALCULATE_PEAK_REPROD` python reporting modules
+* [[#83]](https://github.com/nf-core/cutandrun/issues/83) - Fixed error in violin chart generation with cast to int64
+
+### Software dependencies
+
+Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency | Old version | New version |
+|------------|-------------|-------------|
+| `samtools` | 1.13        | 1.14        |
+
+> **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 version information isn't present.
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -12,7 +12,7 @@
 
 * [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/)
+* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
     > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools