[MODIF] fix md lint

CHANGELOG.md

@@ -12,38 +12,39 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * 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_* cooltools `0.3.2`
-    * *_New_* fanc `0.8.30`
-    * *_Removed_* r-markdown
+  * 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_* cooltools `0.3.2`
+  * *_New_* fanc `0.8.30`
+  * *_Removed_* r-markdown
 
 ### `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`
 
 * 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`
+  * `--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
 

README.md

@@ -43,7 +43,10 @@ sites (bowtie2)
 
 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
 
@@ -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>
 ```
 
-> 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!
 
@@ -63,7 +70,8 @@ See [usage docs](docs/usage.md) for all of the available options when running th
 
 ## 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)
 2. Pipeline configuration
@@ -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).
 
-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
 
@@ -97,7 +107,9 @@ You can cite the `nf-core` publication as follows:
 
 > **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)

environment.yml

 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-hic-1.3.0dev
+name: nf-core-hic-1.2.0dev
 channels:
   - conda-forge
   - bioconda