prettier

Author: nservant

CHANGELOG.md

@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## v1.4.0
 
 ### `Added`
+
 * DSL2 version of nf-core-hic pipeline
 
 ## v1.3.1 - 2021-09-25
@@ -75,21 +76,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   * 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
+  * _*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)
+  are expected to be sorted (sort -m)
 
 ### `Deprecated`
 
@@ -138,7 +139,7 @@ DNase Hi-C, Micro-C, capture-C or HiChip data.
 In summary, this version allows :
 
 * Automatic detection and generation of annotation files based on igenomes
-if not provided.
+  if not provided.
 * Two-steps alignment of raw sequencing reads
 * Reads filtering and detection of valid interaction products
 * Generation of raw contact matrices for a set of resolutions

CITATIONS.md

@@ -1,6 +1,5 @@
 # nf-core/hic: Citations
 
-
 ## [HiC-Pro](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x)
 
 > Servant N, Varoquaux N, Lajoie BR, Viara E, Chen C, Vert JP, Dekker J, Heard E, Barillot E. Genome Biology 2015, 16:259 doi: [10.1186/s13059-015-0831-x](https://dx.doi.org/10.1186/s13059-015-0831-x)
@@ -15,27 +14,26 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
+* [Anaconda](https://anaconda.com)
 
   > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
 
-- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 
   > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
 
-- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
 
   > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
 
-- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
-- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
-

README.md

@@ -23,11 +23,11 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 2. Hi-C data processing
    1. [`HiC-Pro`](https://github.com/nservant/HiC-Pro)
       1. Mapping using a two steps strategy to rescue reads spanning the ligation
-      sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
+         sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
       2. Detection of valid interaction products
       3. Duplicates removal
       4. Generate raw and normalized contact maps ([`iced`](https://github.com/hiclib/iced))
@@ -39,7 +39,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
 8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/))
 9. Quality control report ([`MultiQC`](https://multiqc.info/))
 
-
 ## Quick Start
 
 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
@@ -54,10 +53,10 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
 
-   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
-   > - 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.
-   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
-   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+   > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
+   > * 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.
+   > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
+   > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
 
 4. Start running your own analysis!
 
@@ -81,7 +80,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use  nf-core/hic for your analysis, please cite it using the following doi: doi: [10.5281/zenodo.2669513](https://doi.org/10.5281/zenodo.2669513)
+If you use nf-core/hic for your analysis, please cite it using the following doi: doi: [10.5281/zenodo.2669513](https://doi.org/10.5281/zenodo.2669513)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

docs/output.md

@@ -20,9 +20,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   * [Compartments calling](#compartments-calling)
   * [TADs calling](#tads-calling)
 * [MultiQC](#multiqc) - aggregate report and quality controls, describing
-results of the whole pipeline
+  results of the whole pipeline
 * [Export](#exprot) - additionnal export for compatibility with downstream
-analysis tool and visualization
+  analysis tool and visualization
 
 ## HiC-Pro
 
@@ -79,14 +79,14 @@ reference genome and the digestion protocol.
 Invalid pairs are classified as follow:
 
 * Dangling end, i.e. unligated fragments (both reads mapped on the same
-restriction fragment)
+  restriction fragment)
 * Self circles, i.e. fragments ligated on themselves (both reads mapped on the
-same restriction fragment in inverted orientation)
+  same restriction fragment in inverted orientation)
 * Religation, i.e. ligation of juxtaposed fragments
 * Filtered pairs, i.e. any pairs that do not match the filtering criteria on
-inserts size, restriction fragments size
+  inserts size, restriction fragments size
 * Dumped pairs, i.e. any pairs for which we were not able to reconstruct the
-ligation product.
+  ligation product.
 
 Only valid pairs involving two different restriction fragments are used to
 build the contact maps.
@@ -249,10 +249,10 @@ Usually, TADs results are presented as simple BED files, or bigWig files, with t
 <details markdown="1">
 <summary>Output files</summary>
 
-- `multiqc/`
-  - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-  - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-  - `multiqc_plots/`: directory containing static images from the report in various formats.
+* `multiqc/`
+  * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+  * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+  * `multiqc_plots/`: directory containing static images from the report in various formats.
 
 </details>
 
@@ -265,10 +265,10 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 <details markdown="1">
 <summary>Output files</summary>
 
-- `pipeline_info/`
-  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
-  - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+* `pipeline_info/`
+  * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+  * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
+  * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
 
 </details>
 

docs/usage.md

@@ -102,7 +102,7 @@ fails after three times then the pipeline is stopped.
 ## Core Nextflow arguments
 
 > **NB:** These options are part of Nextflow and use a _single_ hyphen
-(pipeline parameters use a double-hyphen).
+> (pipeline parameters use a double-hyphen).
 
 ### `-profile`
 
@@ -112,7 +112,7 @@ configuration presets for different compute environments.
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/).
 
 > We highly recommend the use of Docker or Singularity containers for full
-pipeline reproducibility, however when this is not possible, Conda is also supported.
+> pipeline reproducibility, however when this is not possible, Conda is also supported.
 
 The pipeline also dynamically loads configurations from
 [https://github.com/nf-core/configs](https://github.com/nf-core/configs)
@@ -131,21 +131,21 @@ If `-profile` is not specified, the pipeline will run locally and
 expect all software to be
 installed and available on the `PATH`. This is _not_ recommended.
 
-- `docker`
-  - A generic configuration profile to be used with [Docker](https://docker.com/)
-- `singularity`
-  - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
-- `podman`
-  - A generic configuration profile to be used with [Podman](https://podman.io/)
-- `shifter`
-  - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
-- `charliecloud`
-  - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
-- `conda`
-  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
-- `test`
-  - A profile with a complete configuration for automated testing
-  - Includes links to test data so needs no other parameters
+* `docker`
+  * A generic configuration profile to be used with [Docker](https://docker.com/)
+* `singularity`
+  * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
+* `podman`
+  * A generic configuration profile to be used with [Podman](https://podman.io/)
+* `shifter`
+  * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
+* `charliecloud`
+  * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+* `conda`
+  * A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
+* `test`
+  * A profile with a complete configuration for automated testing
+  * Includes links to test data so needs no other parameters
 
 ### `-resume`
 
@@ -224,7 +224,7 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
 2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
 3. Create the custom config accordingly:
 
-   - For Docker:
+   * For Docker:
 
      ```nextflow
      process {
@@ -234,7 +234,7 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
      }
      ```
 
-   - For Singularity:
+   * For Singularity:
 
      ```nextflow
      process {
@@ -244,7 +244,7 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
      }
      ```
 
-   - For Conda:
+   * For Conda:
 
      ```nextflow
      process {
@@ -330,7 +330,7 @@ Please note the following requirements:
 1. The path must be enclosed in quotes
 2. The path must have at least one `*` wildcard character
 3. When using the pipeline with paired end data, the path must use `{1,2}`
-notation to specify read pairs.
+   notation to specify read pairs.
 
 If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
 
@@ -467,7 +467,7 @@ Minimum mapping quality. Reads with lower quality are discarded. Default: 10
 
 This parameter allows to automatically set the `--restriction_site` and
 `--ligation_site` parameter according to the restriction enzyme you used.
-Available keywords are  'hindiii', 'dpnii', 'mboi', 'arima'.
+Available keywords are 'hindiii', 'dpnii', 'mboi', 'arima'.
 
 ```bash
 --digestion 'hindiii'

modules.json

@@ -23,4 +23,4 @@
             }
         }
     }
-}
+}