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Commit b3459665 authored by nservant's avatar nservant
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[MODIF] fix md lint

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...@@ -32,7 +32,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ...@@ -32,7 +32,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Fixed` ### `Fixed`
* Sort output of `get_valid_interaction` process as the input files of `remove_duplicates` are expected to be sorted (sort -m) * Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
are expected to be sorted (sort -m)
### `Deprecated` ### `Deprecated`
......
...@@ -43,7 +43,10 @@ sites (bowtie2) ...@@ -43,7 +43,10 @@ sites (bowtie2)
i. Install [`nextflow`](https://nf-co.re/usage/installation) i. Install [`nextflow`](https://nf-co.re/usage/installation)
ii. Install either [`Docker`](https://docs.docker.com/engine/installation/) or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) 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)) ii. Install either [`Docker`](https://docs.docker.com/engine/installation/)
or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/)
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
...@@ -51,7 +54,11 @@ iii. Download the pipeline and test it on a minimal dataset with a single comman ...@@ -51,7 +54,11 @@ iii. Download the pipeline and test it on a minimal dataset with a single comman
nextflow run nf-core/hic -profile test,<docker/singularity/conda/institute> 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. > 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!
...@@ -63,7 +70,8 @@ See [usage docs](docs/usage.md) for all of the available options when running th ...@@ -63,7 +70,8 @@ See [usage docs](docs/usage.md) for all of the available options when running th
## Documentation ## Documentation
The nf-core/hic pipeline comes with documentation about the pipeline, found in the `docs/` directory: The nf-core/hic pipeline comes with documentation about the pipeline,
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
...@@ -86,7 +94,9 @@ nf-core/hic was originally written by Nicolas Servant. ...@@ -86,7 +94,9 @@ 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). 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
[Slack](https://nfcore.slack.com/channels/hic) (you can join with
[this invite](https://nf-co.re/join/slack)).
## Citation ## Citation
...@@ -97,7 +107,9 @@ You can cite the `nf-core` publication as follows: ...@@ -97,7 +107,9 @@ You can cite the `nf-core` publication as follows:
> **The nf-core framework for community-curated bioinformatics pipelines.** > **The nf-core framework for community-curated bioinformatics pipelines.**
> >
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > 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) > ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)
# You can use this file to create a conda environment for this pipeline: # You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml # conda env create -f environment.yml
name: nf-core-hic-1.3.0dev name: nf-core-hic-1.2.0dev
channels: channels:
- conda-forge - conda-forge
- bioconda - bioconda
......
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