Merge pull request #72 from nservant/dev

Bump v1.2.2 - Template fix

.github/.dockstore.yml

+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config

.github/CONTRIBUTING.md

@@ -48,7 +48,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Patch
 
-: warning: Only in the unlikely and regretful event of a release happening with a bug.
+:warning: Only in the unlikely and regretful event of a release happening with a bug.
 
 * On your own fork, make a new branch `patch` based on `upstream/master`.
 * Fix the bug, and bump version (X.Y.Z+1).
@@ -59,3 +59,4 @@ For further information/help, please consult the [nf-core/hic documentation](htt
 don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel
 ([join our Slack here](https://nf-co.re/join/slack)).
 
+For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/hic/docs) and don't hesitate to get in touch on the nf-core Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

+<!--
 # nf-core/hic bug report
 
 Hi there!
 
 Thanks for telling us about a problem with the pipeline.
 Please delete this text and anything that's not relevant from the template below:
+-->
 
-## Describe the bug
+## Description of the bug
 
-A clear and concise description of what the bug is.
+<!-- A clear and concise description of what the bug is. -->
 
 ## Steps to reproduce
 
 Steps to reproduce the behaviour:
 
-1. Command line: `nextflow run ...`
-2. See error: _Please provide your error message_
+1. Command line: <!-- [e.g. `nextflow run ...`] -->
+2. See error: <!-- [Please provide your error message] -->
 
 ## Expected behaviour
 
-A clear and concise description of what you expected to happen.
+<!-- A clear and concise description of what you expected to happen. -->
 
 ## System
 
@@ -39,4 +41,4 @@ A clear and concise description of what you expected to happen.
 
 ## Additional context
 
-Add any other context about the problem here.
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/feature_request.md

+<!--
 # nf-core/hic feature request
 
 Hi there!
@@ -5,20 +6,23 @@ Hi there!
 Thanks for suggesting a new feature for the pipeline!
 Please delete this text and anything that's not relevant from the template below:
 
+-->
+
 ## Is your feature request related to a problem? Please describe
 
-A clear and concise description of what the problem is.
+<!-- A clear and concise description of what the problem is. -->
 
-Ex. I'm always frustrated when [...]
+<!-- e.g. [I'm always frustrated when ...] -->
 
 ## Describe the solution you'd like
 
-A clear and concise description of what you want to happen.
+<!-- A clear and concise description of what you want to happen. -->
 
 ## Describe alternatives you've considered
 
-A clear and concise description of any alternative solutions or features you've considered.
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
 
 ## Additional context
 
-Add any other context about the feature request here.
+<!-- Add any other context about the feature request here. -->
+

.github/PULL_REQUEST_TEMPLATE.md

+<!--
 # nf-core/hic pull request
 
 Many thanks for contributing to nf-core/hic!
@@ -5,15 +6,16 @@ Many thanks for contributing to nf-core/hic!
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
+-->
+
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason)
+- [ ] `CHANGELOG.md` is updated
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If necessary, also make a PR on the [nf-core/hic branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/hic)
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
-- [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Documentation in `docs` is updated
-- [ ] `CHANGELOG.md` is updated
-- [ ] `README.md` is updated
+- [ ] If necessary, also make a PR on the [nf-core/hic branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/hic)
 
-**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
\ No newline at end of file

.github/workflows/awsfulltest.yml

+name: nf-core AWS full size tests
+# This workflow is triggered on push to the master branch.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  run-awstest:
+    name: Run AWS full tests
+    if: github.repository == 'nf-core/hic'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: goanpeca/setup-miniconda@v1.0.2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        # 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 \
+            --job-name nf-core-hic \
+            --job-queue $AWS_JOB_QUEUE \
+            --job-definition $AWS_JOB_DEFINITION \
+            --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/awstest.yml

+name: nf-core AWS test
+# This workflow is triggered on push to the master branch.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  run-awstest:
+    name: Run AWS tests
+    if: github.repository == 'nf-core/hic'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: goanpeca/setup-miniconda@v1.0.2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - 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 \
+          --job-name nf-core-hic \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/branch.yml

@@ -3,14 +3,35 @@ name: nf-core branch protection
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
   pull_request:
-    branches:
-    - master
+    branches: [master]
 
 jobs:
   test:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
-      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
+        if: github.repository == 'nf-core/hic'
         run: |
-          { [[ $(git remote get-url origin) == *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" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ 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 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.
+
+            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.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+

.github/workflows/ci.yml

 name: nf-core CI
-# This workflow is triggered on pushes and PRs to the repository.
-# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on: [push, pull_request]
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
 
 jobs:
   test:
+    name: Run workflow tests
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hic') }}
+    runs-on: ubuntu-latest
     env:
       NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
         nxf_ver: ['19.10.0', '']
     steps:
-      - uses: actions/checkout@v2
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/hic:1.2.2
+
+      - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
+        run: |
+          docker pull nfcore/hic:dev
+          docker tag nfcore/hic:dev nfcore/hic:1.2.2
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-      - name: Pull docker image
-        run: |
-          docker pull nfcore/hic:dev
-          docker tag nfcore/hic:dev nfcore/hic:1.2.1
+
       - name: Run pipeline with test data
         run: |
-          # nf-core: You can customise CI pipeline run tests as required
-          # (eg. adding multiple test runs with different parameters)
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker

.github/workflows/linting.yml

@@ -33,18 +33,33 @@ jobs:
   nf-core:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+
       - uses: actions/setup-python@v1
         with:
           python-version: '3.6'
           architecture: 'x64'
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install nf-core
+
       - name: Run nf-core lint
-        run: nf-core lint ${GITHUB_WORKSPACE}
+        env:
+          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}
+
+      - name: Upload linting log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: linting-log-file
+          path: lint_log.txt

.github/workflows/push_dockerhub.yml

+name: nf-core Docker push
+# This builds the docker image and pushes it to DockerHub
+# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+  release:
+    types: [published]
+
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/hic' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/hic:latest
+
+      - name: Push Docker image to DockerHub (dev)
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker tag nfcore/hic:latest nfcore/hic:dev
+          docker push nfcore/hic:dev
+
+      - name: Push Docker image to DockerHub (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/hic:latest
+          docker tag nfcore/hic:latest nfcore/hic:${{ github.event.release.tag_name }}
+          docker push nfcore/hic:${{ github.event.release.tag_name }}

.gitignore

@@ -5,4 +5,5 @@ results/
 .DS_Store
 tests/
 testing/
+testing*
 *.pyc

CHANGELOG.md

 # nf-core/hic: Changelog
 
-The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
-and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+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).
+
+## v1.2.2 - 2020-08-07
+
+### `Added`
+
+* Template update for nf-core/tools v1.10.2
+
+### `Fixed`
+
+* Bug in `--split_fastq` option not recognized
 
 ## v1.2.1 - 2020-07-06
 

CODE_OF_CONDUCT.md

@@ -70,7 +70,7 @@ members of the project's leadership.
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 1.4, available at
-[http://contributor-covenant.org/version/1/4][version]
+[https://www.contributor-covenant.org/version/1/4/code-of-conduct/][version]
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://contributor-covenant.org
+[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/

Dockerfile

-FROM nfcore/base:1.9
+FROM nfcore/base:1.10.2
+
 LABEL authors="Nicolas Servant" \
       description="Docker image containing all software requirements for the nf-core/hic pipeline"
 
@@ -6,9 +7,14 @@ LABEL authors="Nicolas Servant" \
 RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y
 
 COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-hic-1.2.1/bin:$PATH
+RUN conda env create --quiet -f /environment.yml && conda clean -a
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-hic-1.2.2/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.2.1 > nf-core-hic-1.2.1.yml
+RUN conda env export --name nf-core-hic-1.2.2 > nf-core-hic-1.2.2.yml
 
+# Instruct R processes to use these empty files instead of clashing with a local version
+RUN touch .Rprofile
+RUN touch .Renviron

README.md

@@ -6,10 +6,11 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/hic/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/hic/actions)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
 
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/hic.svg)](https://hub.docker.com/r/nfcore/hic)
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2669513.svg)](https://doi.org/10.5281/zenodo.2669513)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23hic-4A154B?logo=slack)](https://nfcore.slack.com/channels/hic)
 
 ## Introduction
 
@@ -66,7 +67,8 @@ iv. Start running your own analysis!
 nextflow run nf-core/hic -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
 ```
 
-See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
+See [usage docs](docs/usage.md) for all of the available options when running
+the pipeline.
 
 ## Documentation
 
@@ -82,6 +84,10 @@ found in the `docs/` directory:
 4. [Output and how to interpret the results](docs/output.md)
 5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
+The nf-core/hic pipeline comes with documentation about the pipeline which
+you can read at [https://nf-core/hic/docs](https://nf-core/hic/docs) or
+find in the [`docs/` directory](docs).
+
 For further information or help, don't hesitate to get in touch on
 [Slack](https://nfcore.slack.com/channels/hic).
 You can join with [this invite](https://nf-co.re/join/slack).
@@ -94,9 +100,9 @@ nf-core/hic was originally written by Nicolas Servant.
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-For further information or help, don't hesitate to get in touch on
-[Slack](https://nfcore.slack.com/channels/hic) (you can join with
-[this invite](https://nf-co.re/join/slack)).
+For further information or help, don't hesitate to get in touch on the
+[Slack `#hic` channel](https://nfcore.slack.com/channels/hic)
+(you can join with [this invite](https://nf-co.re/join/slack)).
 
 ## Citation
 
@@ -110,6 +116,5 @@ You can cite the `nf-core` publication as follows:
 > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg,
 Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
 >
-> _Nat Biotechnol._ 2020 Feb 13.
-doi:[10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).  
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
 > ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)

bin/markdown_to_html.py

@@ -4,33 +4,23 @@ import argparse
 import markdown
 import os
 import sys
+import io
+
 
 def convert_markdown(in_fn):
-    input_md = open(in_fn, mode="r", encoding="utf-8").read()
+    input_md = io.open(in_fn, mode="r", encoding="utf-8").read()
     html = markdown.markdown(
         "[TOC]\n" + input_md,
-        extensions = [
-            'pymdownx.extra',
-            'pymdownx.b64',
-            'pymdownx.highlight',
-            'pymdownx.emoji',
-            'pymdownx.tilde',
-            'toc'
-        ],
-        extension_configs = {
-            'pymdownx.b64': {
-                'base_path': os.path.dirname(in_fn)
-            },
-            'pymdownx.highlight': {
-                'noclasses': True
-            },
-            'toc': {
-                'title': 'Table of Contents'
-            }
-        }
+        extensions=["pymdownx.extra", "pymdownx.b64", "pymdownx.highlight", "pymdownx.emoji", "pymdownx.tilde", "toc"],
+        extension_configs={
+            "pymdownx.b64": {"base_path": os.path.dirname(in_fn)},
+            "pymdownx.highlight": {"noclasses": True},
+            "toc": {"title": "Table of Contents"},
+        },
     )
     return html
 
+
 def wrap_html(contents):
     header = """<!DOCTYPE html><html>
     <head>
@@ -83,18 +73,19 @@ def wrap_html(contents):
 
 def parse_args(args=None):
     parser = argparse.ArgumentParser()
-    parser.add_argument('mdfile', type=argparse.FileType('r'), nargs='?',
-                        help='File to convert. Defaults to stdin.')
-    parser.add_argument('-o', '--out', type=argparse.FileType('w'),
-                        default=sys.stdout,
-                        help='Output file name. Defaults to stdout.')
+    parser.add_argument("mdfile", type=argparse.FileType("r"), nargs="?", help="File to convert. Defaults to stdin.")
+    parser.add_argument(
+        "-o", "--out", type=argparse.FileType("w"), default=sys.stdout, help="Output file name. Defaults to stdout."
+    )
     return parser.parse_args(args)
 
+
 def main(args=None):
     args = parse_args(args)
     converted_md = convert_markdown(args.mdfile.name)
     html = wrap_html(converted_md)
     args.out.write(html)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     sys.exit(main())

bin/scrape_software_versions.py

@@ -34,7 +34,7 @@ for k, v in regexes.items():
 # Remove software set to false in results
 for k in list(results):
     if not results[k]:
-        del(results[k])
+        del results[k]
 
 # Remove software set to false in results
 for k in results:
@@ -42,7 +42,8 @@ for k in results:
         del(results[k])
 
 # Dump to YAML
-print ('''
+print(
+    """
 id: 'software_versions'
 section_name: 'nf-core/hic Software Versions'
 section_href: 'https://github.com/nf-core/hic'
@@ -50,12 +51,14 @@ plot_type: 'html'
 description: 'are collected at run time from the software output.'
 data: |
     <dl class="dl-horizontal">
-''')
-for k,v in results.items():
-    print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k,v))
-print ("    </dl>")
+"""
+)
+for k, v in results.items():
+    print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k, v))
+print("    </dl>")
 
 # Write out regexes as csv file:
-with open('software_versions.csv', 'w') as f:
-    for k,v in results.items():
-        f.write("{}\t{}\n".format(k,v))
+with open("software_versions.csv", "w") as f:
+    for k, v in results.items():
+        f.write("{}\t{}\n".format(k, v))
+

conf/hicpro.config

@@ -10,7 +10,6 @@
 params {
 
        // Alignment options
-       splitFastq = false
        bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'
        bwt2_opts_trimmed = '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'
        min_mapq = 10
@@ -35,9 +34,5 @@ params {
        ice_filer_low_count_perc = 0.02
        ice_filer_high_count_perc =  0
        ice_eps = 0.1
-
-       saveReference = false
-       saveAlignedIntermediates = false
-       saveInteractionBAM = false
 }
 

conf/test.config

@@ -18,7 +18,7 @@ config_profile_name = 'Hi-C test data from Schalbetter et al. (2017)'
   max_time = 1.h
 
   // Input data
-  readPaths = [
+  input_paths = [
     ['SRR4292758_00', ['https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/data/SRR4292758_00_R2.fastq.gz']]
    ]