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Merge pull request #61 from nf-core/dev

version 1.2.0 nf-core-hic
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# nf-core/hic: Contributing Guidelines # nf-core/hic: Contributing Guidelines
Hi there! Many thanks for taking an interest in improving nf-core/hic. Hi there!
Many thanks for taking an interest in improving nf-core/hic.
We try to manage the required tasks for nf-core/hic using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time. We try to manage the required tasks for nf-core/hic using GitHub issues, you probably came to this page when creating one.
Please use the pre-filled template to save time.
However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) However, don't be put off by this template - other more general issues and suggestions are welcome!
Contributions to the code are even more welcome ;)
> If you need help using or modifying nf-core/hic then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
> If you need help using or modifying nf-core/hic then the best place to ask is on the nf-core
Slack [#hic](https://nfcore.slack.com/channels/hic) channel ([join our Slack here](https://nf-co.re/join/slack)).
## Contribution workflow ## Contribution workflow
If you'd like to write some code for nf-core/hic, the standard workflow
is as follows:
1. Check that there isn't already an issue about your idea in the If you'd like to write some code for nf-core/hic, the standard workflow is as follows:
[nf-core/hic issues](https://github.com/nf-core/hic/issues) to avoid
duplicating work. 1. Check that there isn't already an issue about your idea in the [nf-core/hic issues](https://github.com/nf-core/hic/issues) to avoid duplicating work
* If there isn't one already, please create one so that others know you're working on this * If there isn't one already, please create one so that others know you're working on this
2. Fork the [nf-core/hic repository](https://github.com/nf-core/hic) to your GitHub account 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/hic repository](https://github.com/nf-core/hic) to your GitHub account
3. Make the necessary changes / additions within your forked repository 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. 4. 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 [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
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/).
## Tests ## Tests
When you create a pull request with changes, [Travis CI](https://travis-ci.org/) will run automatic tests.
When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
There are typically two types of tests that run: There are typically two types of tests that run:
### Lint Tests ### Lint Tests
The nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to.
`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command. To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
If any failures or warnings are encountered, please follow the listed URL for more documentation. If any failures or warnings are encountered, please follow the listed URL for more documentation.
### Pipeline Tests ### Pipeline Tests
Each nf-core pipeline should be set up with a minimal set of test-data.
Travis CI then runs the pipeline on this data to ensure that it exists successfully. Each `nf-core` pipeline should be set up with a minimal set of test-data.
`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
If there are any failures then the automated tests fail. If there are any failures then the automated tests fail.
These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code. These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
## Patch
: 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).
* A PR should be made on `master` from patch to directly this particular bug.
## Getting help ## Getting help
For further information/help, please consult the [nf-core/hic documentation](https://github.com/nf-core/hic#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/). For further information/help, please consult the [nf-core/hic documentation](https://nf-co.re/nf-core/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)).
# nf-core/hic bug report
Hi there! 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: 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
#### Describe 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
Steps to reproduce the behaviour: Steps to reproduce the behaviour:
1. Command line: `nextflow run ...` 1. Command line: `nextflow run ...`
2. See error: _Please provide your error message_ 2. See error: _Please provide your error message_
#### Expected behaviour ## 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: ## System
- Hardware: [e.g. HPC, Desktop, Cloud...]
- Executor: [e.g. slurm, local, awsbatch...] - Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
- OS: [e.g. CentOS Linux, macOS, Linux Mint...] - Executor: <!-- [e.g. slurm, local, awsbatch...] -->
- Version [e.g. 7, 10.13.6, 18.3...] - OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
## Nextflow Installation
- Version: <!-- [e.g. 19.10.0] -->
## Container engine
#### Nextflow Installation: - Engine: <!-- [e.g. Conda, Docker or Singularity] -->
- Version: [e.g. 0.31.0] - version: <!-- [e.g. 1.0.0] -->
- Image tag: <!-- [e.g. nfcore/hic:1.0.0] -->
#### Container engine: ## Additional context
- Engine: [e.g. Conda, Docker or Singularity]
- version: [e.g. 1.0.0]
- Image tag: [e.g. nfcore/hic:1.0.0]
#### Additional context
Add any other context about the problem here. Add any other context about the problem here.
# nf-core/hic feature request
Hi there! 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: 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
#### 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 [...] Ex. I'm always frustrated when [...]
#### Describe the solution you'd like ## 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 ## 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 ## Additional context
Add any other context about the feature request here. Add any other context about the feature request here.
Many thanks to contributing to nf-core/hic! # nf-core/hic pull request
Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). 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).
## PR checklist ## 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! - [ ] This comment contains a description of changes (with reason)
- [ ] 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) - [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`). - [ ] 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)
- [ ] Make sure your code lints (`nf-core lint .`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
- [ ] Documentation in `docs` is updated - [ ] Make sure your code lints (`nf-core lint .`).
- [ ] `CHANGELOG.md` is updated - [ ] Documentation in `docs` is updated
- [ ] `README.md` is updated - [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
**Learn more about contributing:** https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md
**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
\ No newline at end of file
# Markdownlint configuration file # Markdownlint configuration file
default: true, default: true,
line-length: false line-length: false
no-multiple-blanks: 0
blanks-around-headers: false
blanks-around-lists: false
header-increment: false
no-duplicate-header: no-duplicate-header:
siblings_only: true siblings_only: true
name: nf-core branch protection
# This workflow is triggered on PRs to master branch on the repository
# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
on:
pull_request:
branches:
- master
jobs:
test:
runs-on: ubuntu-18.04
steps:
# PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
- name: Check PRs
run: |
{ [[ $(git remote get-url origin) == *nf-core/hic ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
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]
jobs:
test:
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: 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:1.2.0
- 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
name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
on:
push:
pull_request:
release:
types: [published]
jobs:
Markdown:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
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
YAML:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/setup-node@v1
with:
node-version: '10'
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Run yaml-lint
run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
nf-core:
runs-on: ubuntu-latest
steps:
- 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}
...@@ -3,5 +3,6 @@ work/ ...@@ -3,5 +3,6 @@ work/
data/ data/
results/ results/
.DS_Store .DS_Store
tests/test_data tests/
testing/
*.pyc *.pyc
sudo: required
language: python
jdk: openjdk8
services: docker
python: '3.6'
cache: pip
matrix:
fast_finish: true
before_install:
- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'
# Pull the docker image first so the test doesn't wait for this
- docker pull nfcore/hic:dev
# Fake the tag locally so that the pipeline runs properly
# Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
- docker tag nfcore/hic:dev nfcore/hic:1.1.0
install:
# Install Nextflow
- mkdir /tmp/nextflow && cd /tmp/nextflow
- wget -qO- get.nextflow.io | bash
- sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
# Install nf-core/tools
- pip install --upgrade pip
- pip install nf-core
# Reset
- mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
# Install markdownlint-cli
- sudo apt-get install npm && npm install -g markdownlint-cli
env:
- NXF_VER='19.04.0' # Specify a minimum NF version that should be tested and work
- NXF_VER='' # Plus: get the latest NF version and check that it works
script:
# Lint the pipeline code
- nf-core lint ${TRAVIS_BUILD_DIR}
# Lint the documentation
- markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
# Run the pipeline with the test profile
- nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
# nf-core/hic: Changelog # 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).
## v1.2.0 - 2020-06-18
### `Added`
* Bump v1.2.0
* Merge template nf-core 1.9
* Move some options to camel_case
* Update python scripts for python3
* Update conda environment file
* python base `2.7.15` > `3.7.6`
* pip `19.1` > `20.0.1`
* scipy `1.2.1` > `1.4.1`
* numpy `1.16.3` > `1.18.1`
* bx-python `0.8.2` > `0.8.8`
* pysam `0.15.2` > `0.15.4`
* cooler `0.8.5` > `0.8.6`
* multiqc `1.7` > `1.8`
* iced `0.5.1` > `0.5.6`
* *_New_* pymdown-extensions `7.1`
* *_New_* hicexplorer `3.4.3`
* *_New_* bioconductor-hitc `1.32.0`
* *_New_* r-optparse `1.6.6`
* *_New_* ucsc-bedgraphtobigwig `377`
* *_New_* cython `0.29.19`
* *_New_* cooltools `0.3.2`
* *_New_* fanc `0.8.30`
* *_Removed_* r-markdown
### `Fixed`
* Fix error in doc for Arima kit usage
* Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
are expected to be sorted (sort -m)
### `Deprecated`
* Command line options converted to `camel_case`:
* `--skipMaps` > `--skip_maps`
* `--skipIce` > `--skip_ice`
* `--skipCool` > `--skip_cool`
* `--skipMultiQC` > `--skip_multiqc`
* `--saveReference` > `--save_reference`
* `--saveAlignedIntermediates` > `--save_aligned_intermediates`
* `--saveInteractionBAM` > `--save_interaction_bam`
## v1.1.1 - 2020-04-02
### `Fixed`
* Fix bug in tag. Remove '['
## v1.1.0 - 2019-10-15 ## v1.1.0 - 2019-10-15
### `Added`
* Update hicpro2higlass with `-p` parameter
* Support 'N' base motif in restriction/ligation sites * Support 'N' base motif in restriction/ligation sites
* Support multiple restriction enzymes/ligattion sites (comma separated) ([#31](https://github.com/nf-core/hic/issues/31)) * Support multiple restriction enzymes/ligattion sites (comma separated) ([#31](https://github.com/nf-core/hic/issues/31))
* Add --saveInteractionBAM option * Add --saveInteractionBAM option
* Add DOI ([#29](https://github.com/nf-core/hic/issues/29)) * Add DOI ([#29](https://github.com/nf-core/hic/issues/29))
* Fix bug for reads extension _1/_2 ([#30](https://github.com/nf-core/hic/issues/30))
* Update manual ([#28](https://github.com/nf-core/hic/issues/28)) * Update manual ([#28](https://github.com/nf-core/hic/issues/28))
## v1.0 - 2019-05-06 ### `Fixed`
* Fix bug for reads extension `_1`/`_2` ([#30](https://github.com/nf-core/hic/issues/30))
## v1.0 - [2019-05-06]
Initial release of nf-core/hic, created with the [nf-core](http://nf-co.re/) template.
### `Added`
First version of nf-core Hi-C pipeline which is a Nextflow implementation of First version of nf-core Hi-C pipeline which is a Nextflow implementation of
the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/). the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).
......
...@@ -56,7 +56,7 @@ project may be further defined and clarified by project maintainers. ...@@ -56,7 +56,7 @@ project may be further defined and clarified by project maintainers.
Instances of abusive, harassing, or otherwise unacceptable behavior may be Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported by contacting the project team on reported by contacting the project team on
[Slack](https://nf-core-invite.herokuapp.com/). The project team will review [Slack](https://nf-co.re/join/slack). The project team will review
and investigate all complaints, and will respond in a way that it deems and investigate all complaints, and will respond in a way that it deems
appropriate to the circumstances. The project team is obligated to maintain appropriate to the circumstances. The project team is obligated to maintain
confidentiality with regard to the reporter of an incident. Further details confidentiality with regard to the reporter of an incident. Further details
......
FROM nfcore/base:1.7 FROM nfcore/base:1.9
LABEL authors="Nicolas Servant" \ LABEL authors="Nicolas Servant" \
description="Docker image containing all requirements for nf-core/hic pipeline" description="Docker image containing all software requirements for the nf-core/hic pipeline"
## Install gcc for pip iced install ## Install gcc for pip iced install
RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y
COPY environment.yml / COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-hic-1.1.0/bin:$PATH ENV PATH /opt/conda/envs/nf-core-hic-1.2.0/bin:$PATH
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-hic-1.2.0 > nf-core-hic-1.2.0.yml
...@@ -2,12 +2,12 @@ ...@@ -2,12 +2,12 @@
**Analysis of Chromosome Conformation Capture data (Hi-C)**. **Analysis of Chromosome Conformation Capture data (Hi-C)**.
[![Build Status](https://travis-ci.com/nf-core/hic.svg?branch=master)](https://travis-ci.com/nf-core/hic) [![GitHub Actions CI Status](https://github.com/nf-core/hic/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/hic/actions)
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.04.0-brightgreen.svg)](https://www.nextflow.io/) [![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)](http://bioconda.github.io/)
[![Docker](https://img.shields.io/docker/automated/nfcore/hic.svg)](https://hub.docker.com/r/nfcore/hic) [![Docker](https://img.shields.io/docker/automated/nfcore/hic.svg)](https://hub.docker.com/r/nfcore/hic)
![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2669513.svg)](https://doi.org/10.5281/zenodo.2669513) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2669513.svg)](https://doi.org/10.5281/zenodo.2669513)
...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
This pipeline is based on the This pipeline is based on the
[HiC-Pro workflow](https://github.com/nservant/HiC-Pro). [HiC-Pro workflow](https://github.com/nservant/HiC-Pro).
It was designed to process Hi-C data from raw fastq files (paired-end Illumina It was designed to process Hi-C data from raw FastQ files (paired-end Illumina
data) to normalized contact maps. data) to normalized contact maps.
The current version supports most protocols, including digestion protocols as The current version supports most protocols, including digestion protocols as
well as protocols that do not require restriction enzymes such as DNase Hi-C. well as protocols that do not require restriction enzymes such as DNase Hi-C.
...@@ -43,28 +43,35 @@ sites (bowtie2) ...@@ -43,28 +43,35 @@ sites (bowtie2)
i. Install [`nextflow`](https://nf-co.re/usage/installation) i. Install [`nextflow`](https://nf-co.re/usage/installation)
ii. Install one of [`docker`](https://docs.docker.com/engine/installation/), ii. Install either [`Docker`](https://docs.docker.com/engine/installation/)
[`singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/)
[`conda`](https://conda.io/miniconda.html) for full pipeline reproducibility (please only use [`Conda`](https://conda.io/miniconda.html)
as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))
iii. Download the pipeline and test it on a minimal dataset with a single command iii. Download the pipeline and test it on a minimal dataset with a single command
```bash ```bash
nextflow run hic -profile test,<docker/singularity/conda> nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute>
``` ```
> Please check [nf-core/configs](https://github.com/nf-core/configs#documentation)
to see if a custom config file to run nf-core pipelines already exists for your Institute.
If so, you can simply use `-profile <institute>` in your command.
This will enable either `docker` or `singularity` and set the appropriate execution
settings for your local compute environment.
iv. Start running your own analysis! iv. Start running your own analysis!
```bash ```bash
nextflow run hic -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37 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 ## Documentation
The nf-core/hic pipeline comes with documentation about the pipeline, found in The nf-core/hic pipeline comes with documentation about the pipeline,
the `docs/` directory: found in the `docs/` directory:
1. [Installation](https://nf-co.re/usage/installation) 1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration 2. Pipeline configuration
...@@ -75,27 +82,34 @@ the `docs/` directory: ...@@ -75,27 +82,34 @@ the `docs/` directory:
4. [Output and how to interpret the results](docs/output.md) 4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting) 5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
## Contributions and Support
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 For further information or help, don't hesitate to get in touch on
[Slack](https://nfcore.slack.com/channels/hic). [Slack](https://nfcore.slack.com/channels/hic).
You can join with [this invite](https://nf-co.re/join/slack). You can join with [this invite](https://nf-co.re/join/slack).
## Credits ## Credits
nf-core/hic was originally written by Nicolas Servant. nf-core/hic was originally written by Nicolas Servant.
## Contributions and Support
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)).
## Citation ## Citation
If you use nf-core/hic for your analysis, please cite it using the following If you use nf-core/hic for your analysis, please cite it using the following
doi: [10.5281/zenodo.2669513](https://doi.org/10.5281/zenodo.2669513) doi: [10.5281/zenodo.2669513](https://doi.org/10.5281/zenodo.2669513)
You can cite the `nf-core` pre-print as follows: You can cite the `nf-core` publication as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di
Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. > **The nf-core framework for community-curated bioinformatics pipelines.**
*bioRxiv*. 2019. p. 610741. >
[doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1). > 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).
> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)
...@@ -11,6 +11,8 @@ ...@@ -11,6 +11,8 @@
<body> <body>
<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;"> <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
<img src="cid:nfcorepipelinelogo">
<h1>nf-core/hic v${version}</h1> <h1>nf-core/hic v${version}</h1>
<h2>Run Name: $runName</h2> <h2>Run Name: $runName</h2>
......
======================================== ----------------------------------------------------
nf-core/hic v${version} ,--./,-.
======================================== ___ __ __ __ ___ /,-._.--~\\
|\\ | |__ __ / ` / \\ |__) |__ } {
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
`._,._,'
nf-core/hic v${version}
----------------------------------------------------
Run Name: $runName Run Name: $runName
<% if (success){ <% if (success){
......
...@@ -3,7 +3,9 @@ report_comment: > ...@@ -3,7 +3,9 @@ report_comment: >
analysis pipeline. For information about how to interpret these results, please see the analysis pipeline. For information about how to interpret these results, please see the
<a href="https://github.com/nf-core/hic" target="_blank">documentation</a>. <a href="https://github.com/nf-core/hic" target="_blank">documentation</a>.
report_section_order: report_section_order:
nf-core/hic-software-versions: software_versions:
order: -1000 order: -1000
nf-core-hic-summary:
order: -1001
export_plots: true export_plots: true
assets/nf-core-hic_logo.png

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assets/nf-core-hic_social_preview.png

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