nf-core · ggabernet · Jul 16, 2021 · Jul 13, 2021 · Jul 13, 2021 · Jul 14, 2021
diff --git a/.editorconfig b/.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
+
+# 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
+
+[/assets/*.Rmd]
+indent_size = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -74,7 +74,7 @@ If you wish to contribute a new step, please use the following coding standards:
 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`.

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -18,7 +18,7 @@ Please delete this text and anything that's not relevant from the template below
 I have checked the following places for your error:
 
 - [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-- [ ] [nf-core/bcellmagic pipeline documentation](https://nf-co.re/nf-core/bcellmagic/usage)
+- [ ] [nf-core/bcellmagic pipeline documentation](https://nf-co.re/bcellmagic/usage)
 
 ## Description of the bug
 
@@ -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. nfcore/bcellmagic:1.0.0] -->
 
 ## Additional context
 

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -16,8 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/bcel
 
 - [ ] 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/>nf-core/bcellmagic/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bcellmagic/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/bcellmagic _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`).

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -1,41 +1,30 @@
 name: nf-core AWS full size tests
 # This workflow is triggered on published releases.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   release:
     types: [published]
   workflow_dispatch:
-
-
-env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
-
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS full tests
     if: github.repository == 'nf-core/bcellmagic'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
         with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        run: |
-          aws batch submit-job \
-            --region eu-west-1 \
-            --job-name nf-core-bcellmagic \
-            --job-queue $AWS_JOB_QUEUE \
-            --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/bcellmagic", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/bcellmagic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/bcellmagic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bcellmagic/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bcellmagic/results-${{ github.sha }}"
+            }
+          profiles: '[ "test_full", "aws_tower" ]'
+
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -1,39 +1,28 @@
 name: nf-core AWS test
-# This workflow is triggered on push to the master branch.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
-# It runs the -profile 'test' on AWS batch.
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
 
 on:
   workflow_dispatch:
-
-
-env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
-
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS tests
     if: github.repository == 'nf-core/bcellmagic'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
+
         with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        run: |
-          aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-bcellmagic \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/bcellmagic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/bcellmagic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/bcellmagic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bcellmagic/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bcellmagic/results-${{ github.sha }}"
+            }
+          profiles: '[ "test", "aws_tower" ]'
+
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -18,7 +18,7 @@ jobs:
       - 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:
 
@@ -46,6 +46,20 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-node@v1
+        with:
+          node-version: "10"
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
 
   YAML:
     runs-on: ubuntu-latest
@@ -84,7 +98,6 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
-
   nf-core:
     runs-on: ubuntu-latest
     steps:
@@ -114,7 +127,7 @@ 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() }}

diff --git a/.gitignore b/.gitignore
@@ -3,11 +3,11 @@ work/
 data/
 results/
 .DS_Store
-tests/
 testing/
 testing*
 *.pyc
 node_modules/
 package-lock.json
 .idea/
-nf-params.json
+nf-params.json
+.vscode/
diff --git a/.github/markdownlint.yml → .markdownlint.yml b/.github/markdownlint.yml → .markdownlint.yml
@@ -1,6 +1,8 @@
 # Markdownlint configuration file
 default: true
 line-length: false
+ul-indent:
+    indent: 4
 no-duplicate-header:
     siblings_only: true
 no-inline-html:

diff --git a/.nf-core-lint.yml → .nf-core.yml b/.nf-core-lint.yml → .nf-core.yml
@@ -4,4 +4,4 @@ actions_awsfulltest: False
 params_used: False
 files_exist:
   - environment.yml
-  - Dockerfile
+  - Dockerfile
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#114](https://github.com/nf-core/bcellmagic/pull/114): Added Bcellmagic html report.
 * [#114](https://github.com/nf-core/bcellmagic/pull/114): Improved documentation on amplicon protocol support.
 * [#115](https://github.com/nf-core/bcellmagic/pull/115): Improved output file structure and documentation.
+* [#124](https://github.com/nf-core/bcellmagic/pull/124): Template updte to nf-core tools v2.0.1
 
 ### `Fixed`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -0,0 +1,44 @@
+# nf-core/bcellmagic: 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.
+
+* [pRESTO](https://doi.org/10.1093/bioinformatics/btu138)
+    > Vander Heiden, J. A., Yaari, G., Uduman, M., Stern, J. N. H., O’Connor, K. C., Hafler, D. A., … Kleinstein, S. H. (2014). pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics, 30(13), 1930–1932.
+
+* [SHazaM, Change-O](https://doi.org/10.1093/bioinformatics/btv359)
+    > Gupta, N. T., Vander Heiden, J. A., Uduman, M., Gadala-Maria, D., Yaari, G., & Kleinstein, S. H. (2015). Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. Bioinformatics, 31(20), 3356–3358.
+
+* [Alakazam](https://doi.org/10.1126/scitranslmed.3008879)
+    > Stern, J. N. H., Yaari, G., Vander Heiden, J. A., Church, G., Donahue, W. F., Hintzen, R. Q., … O’Connor, K. C. (2014). B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Science Translational Medicine, 6(248).
+
+* [TIgGER](https://doi.org/10.1073/pnas.1417683112)
+    > Gadala-maria, D., Yaari, G., Uduman, M., & Kleinstein, S. H. (2015). Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proceedings of the National Academy of Sciences, 112(8), 1–9.
+
+## 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.