Prepare release 2.0

.editorconfig

@@ -0,0 +1,27 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[*.json]
+insert_final_newline = unset
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset

.github/CONTRIBUTING.md

@@ -16,8 +16,9 @@ If you'd like to write some code for qbic-pipelines/cellranger, the standard wor
 1. Check that there isn't already an issue about your idea in the [qbic-pipelines/cellranger issues](https://github.com/qbic-pipelines/cellranger/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 [qbic-pipelines/cellranger repository](https://github.com/qbic-pipelines/cellranger) to your GitHub account
-3. Make the necessary changes / additions within your forked repository
-4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+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).
+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/).
 
@@ -66,12 +67,12 @@ 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 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 .`).
+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.yaml`.
+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`.
@@ -80,7 +81,7 @@ 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 schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -51,13 +51,12 @@ Have you provided the following extra information/files:
 
 ## Nextflow Installation
 
-- Version: <!-- [e.g. 19.10.0] -->
+- Version: <!-- [e.g. 21.04.0] -->
 
 ## Container engine
 
 - Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. qbicpipelines/cellranger:1.0.0] -->
 
 ## Additional context
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,10 +16,9 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/qbic-pipelin
 
 - [ ] 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 - add to the software_versions process and a regex to `scrape_software_versions.py`
-    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](<https://github.com/qbic-pipelines/cellranger/tree/master/.github/CONTRIBUTING.md)
-    - [ ] If necessary, also make a PR on the nf-core/qbic-pipelines-cellranger _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint .`).
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cellranger/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also add test datasets on the test-datasets folder.
+- [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/branch.yml

@@ -15,7 +15,6 @@ jobs:
         run: |
           { [[ ${{github.event.pull_request.head.repo.full_name}} == qbic-pipelines/cellranger ]] && [[ $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
       - name: Post PR comment
@@ -33,14 +32,13 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
-            The `master` branch on qbic-pipelines repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
+            The `master` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-

.github/workflows/ci.yml

@@ -23,16 +23,11 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.04.1', '']
+        nxf_ver: ["21.04.1", ""]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Pull docker image
-        run: |
-          docker pull qbicpipelines/cellranger:dev
-          docker tag qbicpipelines/cellranger:dev qbicpipelines/cellranger:1.0
-
       - name: Install Nextflow
         env:
           CAPSULE_LOG: none
@@ -55,17 +50,12 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.04.1', '']
-        profile: ['test_genome']
+        nxf_ver: ["21.04.1", ""]
+        profile: ["test_genome"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Pull docker image
-        run: |
-          docker pull qbicpipelines/cellranger:dev
-          docker tag qbicpipelines/cellranger:dev qbicpipelines/cellranger:1.0
-
       - name: Install Nextflow
         env:
           CAPSULE_LOG: none

.github/workflows/linting.yml

@@ -14,11 +14,11 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-node@v1
         with:
-          node-version: '10'
+          node-version: "10"
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
-        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+        run: markdownlint .
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -35,8 +35,8 @@ jobs:
                 * On Mac: `brew install markdownlint-cli`
                 * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
             * Fix the markdown errors
-                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
-                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
+                * Automatically: `markdownlint . --fix`
+                * Manually resolve anything left from `markdownlint .`
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
 
@@ -46,14 +46,13 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
-
   YAML:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
       - uses: actions/setup-node@v1
         with:
-          node-version: '10'
+          node-version: "10"
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
@@ -84,11 +83,9 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
-
   nf-core:
     runs-on: ubuntu-latest
     steps:
-
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
@@ -101,8 +98,8 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: '3.6'
-          architecture: 'x64'
+          python-version: "3.6"
+          architecture: "x64"
 
       - name: Install dependencies
         run: |
@@ -114,7 +111,7 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
@@ -129,4 +126,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-

.gitignore

@@ -7,4 +7,5 @@ tests/
 testing/
 testing*
 *.pyc
-cellranger*
+cellranger*.tar.gz
+.vscode/

.markdownlint.yml

@@ -0,0 +1,14 @@
+# Markdownlint configuration file
+default: true
+line-length: false
+ul-indent:
+    indent: 4
+no-duplicate-header:
+    siblings_only: true
+no-inline-html:
+    allowed_elements:
+        - img
+        - p
+        - kbd
+        - details
+        - summary

.nf-core.yml

@@ -0,0 +1,22 @@
+lint:
+  files_unchanged:
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/bug_report.md
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/ISSUE_TEMPLATE/feature_request.md
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting.yml
+    - assets/email_template.html
+    - assets/email_template.txt
+    - assets/sendmail_template.txt
+    - assets/multiqc_config.yaml
+    - bin/scrape_software_versions.py
+    - CODE_OF_CONDUCT.md
+    - docs/README.md
+    - .gitignore
+  files_exist:
+    - assets/nf-core-qbic-pipelines/cellranger_logo.png
+    - docs/images/nf-core-qbic-pipelines/cellranger_logo.png
+  actions_ci: False
+  nextflow_config: False

CHANGELOG.md

@@ -3,6 +3,28 @@
 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).
 
+## v2.0dev -
+
+* Ported pipeline to Nextflow DSL2.
+
+### `Added`
+
+* Bump versions 2.0.
+* `cellranger_mode` parameter, allows to select the cellranger operation mode: `GEX` or `multi` are supported.
+
+### `Fixed`
+
+* Fixed channel issues when not providing a reference file.
+
+### `Dependencies`
+
+* Updated GRCh38 cellranger GEX reference
+* Created new container for Cell Ranger, updated version to `6.0.2`.
+
+### `Deprecated`
+
+* `index_file` parameter is deprecated as it is no longer needed.
+
 ## v1.0.1 - Mordor - patch
 
 ### `Added`

CITATIONS.md

@@ -0,0 +1,35 @@
+# nf-core/cellranger: Citations
+
+## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+## Pipeline tools
+
+* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/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.
+
+* [10x Genomics Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
+    > Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun 8, 14049 (2017). doi: 10.1038/ncomms14049.
+
+## Software packaging/containerisation tools
+
+* [Anaconda](https://anaconda.com)
+    > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+
+* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+    > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+
+* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+    > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+    > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

CODE_OF_CONDUCT.md

@@ -44,7 +44,7 @@ The safety officer in consultation with the nf-core core team have the right and
 
 Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC.
 
-## When and where does this Code of Conduct apply
+## When are where does this Code of Conduct apply?
 
 Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: