Merge pull request nf-core#97 from nservant/dev

new pre-release

.github/.dockstore.yml

@@ -3,3 +3,4 @@ version: 1.2
 workflows:
   - subclass: nfl
     primaryDescriptorPath: /nextflow.config
+    publish: True

.github/CONTRIBUTING.md

@@ -69,7 +69,7 @@ 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 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`.
@@ -87,7 +87,7 @@ Once there, use `nf-core 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/%7B%7Bcookiecutter.name_noslash%7D%7D/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/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.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -55,7 +55,7 @@ Have you provided the following extra information/files:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
 

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,6 @@
 ---
 name: Feature request
-about: Suggest an idea for the nf-core website
+about: Suggest an idea for the nf-core/hic pipeline
 labels: enhancement
 ---
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,18 +10,18 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
 -->
+<!-- markdownlint-disable ul-indent -->
 
 ## PR checklist
 
 - [ ] 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/hic/tree/master/.github/CONTRIBUTING.md)
- - [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+    - [ ] 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/hic/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/hic _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`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.
 - [ ] `README.md` is updated (including new tool citations and authors/contributors).
-

.github/workflows/awsfulltest.yml

@@ -9,6 +9,16 @@ on:
     types: [completed]
   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:
     name: Run AWS full tests
@@ -26,13 +36,6 @@ jobs:
         # 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
         # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
-        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 }}
         run: |
           aws batch submit-job \
             --region eu-west-1 \

.github/workflows/awstest.yml

@@ -6,6 +6,16 @@ name: nf-core AWS test
 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:
     name: Run AWS tests
@@ -22,13 +32,6 @@ jobs:
       - name: Start AWS batch job
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
-        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 }}
         run: |
           aws batch submit-job \
           --region eu-west-1 \

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/hic'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
 
       # If the above check failed, post a comment on the PR explaining the failure
@@ -23,13 +23,22 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
+            ## This PR is against the `master` branch :x:
+
+            * Do not close this PR
+            * Click _Edit_ and change the `base` to `dev`
+            * This CI test will remain failed until you push a new commit
+
+            ---
+
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            It looks like this pull-request is has been made against the [${{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 ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the [${{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 }}

.github/workflows/ci.yml

@@ -8,6 +8,9 @@ on:
   release:
     types: [published]
 
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
 jobs:
   test:
     name: Run workflow tests

.github/workflows/linting.yml

@@ -19,6 +19,34 @@ jobs:
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Markdown linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `markdownlint-cli`
+                * 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`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+
   YAML:
     runs-on: ubuntu-latest
     steps:
@@ -29,7 +57,34 @@ jobs:
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## YAML linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `yaml-lint`
+                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
+            * Fix the markdown errors
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                * Fix any reported errors in your YAML files
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
@@ -69,8 +124,9 @@ jobs:
         if: ${{ always() }}
         uses: actions/upload-artifact@v2
         with:
-          name: linting-log-file
+          name: linting-logs
           path: |
             lint_log.txt
             lint_results.md
             PR_number.txt
+

CHANGELOG.md

@@ -5,14 +5,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.3.0dev
 
-* Add HiCExplorer distance decay quality control
-* Add HiCExplorer TADs calling
-* Add insulation score TADs calling
-* Generate cooler/h5/txt contact maps
+* Fix bug in stats export
+* Change the /tmp/ folder by ./tmp/ folder so that all tmp files are now in the work (#24)
+* Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
+* Add HiCExplorer distance decay quality control (#54)
+* Add HiCExplorer TADs calling (#55)
+* Add insulation score TADs calling (#55)
+* Generate cooler/txt contact maps
 * Normalize Hi-C data with cooler instead of iced
 * New `--digestion` parameter to automatically set the restriction_site and ligation_site motifs
 * New `--keep_multi` and `keep_dup` options. Default: false
-* Template update for nf-core/tools v1.11
+* Template update for nf-core/tools
 * Minor fix to summary log messages in pipeline header
 
 ### `Fixed`