From b3459665265ff00e54418a4572cfe44d54bc4c10 Mon Sep 17 00:00:00 2001 From: nservant <nicolas.servant@curie.fr> Date: Wed, 20 May 2020 11:04:36 +0200 Subject: [PATCH] [MODIF] fix md lint --- CHANGELOG.md | 51 +++++++++++++++++++++++++------------------------ README.md | 24 +++++++++++++++++------ environment.yml | 2 +- 3 files changed, 45 insertions(+), 32 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 34cdbc8..6480cc4 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/README.md b/README.md index c8e13a9..be3889d 100644 --- a/README.md +++ b/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) diff --git a/environment.yml b/environment.yml index 7bbaff2..f9c9548 100644 --- a/environment.yml +++ b/environment.yml @@ -1,6 +1,6 @@ # 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 -- GitLab