Merge pull request #111 from drpatelh/master

Update markdownlint checks

Author: apeltzer

.github/CONTRIBUTING.md

@@ -26,7 +26,7 @@ If you're not used to this workflow with git, you can start with some [basic doc
 
 
 ## 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, [Travis CI](https://travis-ci.com/) 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.
 
 There are typically two types of tests that run:

.github/markdownlint.yml

@@ -1,9 +1,5 @@
 # Markdownlint configuration file
 default: true,
 line-length: false
-no-multiple-blanks: 0
-blanks-around-headers: false
-blanks-around-lists: false
-header-increment: false
 no-duplicate-header:
     siblings_only: true

README.md

@@ -1,6 +1,6 @@
 # ![nf-core/chipseq](docs/images/nf-core-chipseq_logo.png)
 
-[![Build Status](https://travis-ci.org/nf-core/chipseq.svg?branch=master)](https://travis-ci.org/nf-core/chipseq)
+[![Build Status](https://travis-ci.com/nf-core/chipseq.svg?branch=master)](https://travis-ci.com/nf-core/chipseq)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.04.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
@@ -54,13 +54,15 @@ ii. Install one of [`docker`](https://docs.docker.com/engine/installation/), [`s
 iii. Download the pipeline and test it on a minimal dataset with a single command
 
 ```bash
-nextflow run nf-core/chipseq -profile test,<docker/singularity/conda>
+nextflow run nf-core/chipseq -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!
 
 ```bash
-nextflow run nf-core/chipseq -profile <docker/singularity/conda> --input design.csv --genome GRCh37
+nextflow run nf-core/chipseq -profile <docker/singularity/conda/institute> --input design.csv --genome GRCh37
 ```
 
 See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
@@ -98,4 +100,3 @@ You can cite the `nf-core` pre-print 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**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
 
 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

@@ -3,6 +3,7 @@
 This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
 
 ## Pipeline overview
+
 The pipeline is built using [Nextflow](https://www.nextflow.io/). See [`main README.md`](../README.md) for a condensed overview of the steps in the pipeline, and the bioinformatics tools used at each step.
 
 See [Illumina website](https://emea.illumina.com/techniques/sequencing/dna-sequencing/chip-seq.html) for more information regarding the ChIP-seq protocol, and for an extensive list of publications.

docs/usage.md

@@ -66,8 +66,8 @@
   * [`--multiqc_config`](#--multiqc_config)
 <!-- TOC END -->
 
-
 ## Introduction
+
 Nextflow handles job submissions on SLURM or other environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through `screen` / `tmux` or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.
 
 It is recommended to limit the Nextflow Java virtual machines memory. We recommend adding the following line to your environment (typically in `~/.bashrc` or `~./bash_profile`):
@@ -77,6 +77,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
 ```
 
 ## Running the pipeline
+
 The typical command for running the pipeline is as follows:
 
 ```bash
@@ -95,23 +96,25 @@ results         # Finished results (configurable, see below)
 ```
 
 ### Updating the pipeline
+
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
 ```bash
 nextflow pull nf-core/chipseq
 ```
 
 ### Reproducibility
+
 It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
 First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
 
-
 ## Main arguments
 
 ### `-profile`
+
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. Note that multiple profiles can be loaded, for example: `-profile docker` - the order of arguments is important!
 
 If `-profile` is not specified at all the pipeline will be run locally and expects all software to be installed and available on the `PATH`.
@@ -132,6 +135,7 @@ If `-profile` is not specified at all the pipeline will be run locally and expec
   * Includes links to test data so needs no other parameters
 
 ### `--input`
+
 You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row as shown in the examples below.
 
 ```bash
@@ -217,24 +221,29 @@ Example design files have been provided with the pipeline for [paired-end](../as
 ## Generic arguments
 
 ### `--single_end`
+
 By default, the pipeline expects paired-end data. If you have single-end data, specify `--single_end` on the command line when you launch the pipeline.
 
 It is not possible to run a mixture of single-end and paired-end files in one run.
 
 ### `--seq_center`
+
 Sequencing center information that will be added to read groups in BAM files.
 
 ### `--fragment_size`
+
 Number of base pairs to extend single-end reads when creating bigWig files (Default: `200`).
 
 ### `--fingerprint_bins`
+
 Number of genomic bins to use when generating the deepTools fingerprint plot. Larger numbers will give a smoother profile, but take longer to run (Default: `500000`).
 
 ## Reference genomes
 
 The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.
 
 ### `--genome` (using iGenomes)
+
 There are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.
 
 You can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:
@@ -266,61 +275,71 @@ params {
 ```
 
 ### `--fasta`
+
 Full path to fasta file containing reference genome (*mandatory* if `--genome` is not specified). If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.
 
 ```bash
 --fasta '[path to FASTA reference]'
 ```
 
 ### `--gtf`
+
 The full path to GTF file for annotating peaks (*mandatory* if `--genome` is not specified). Note that the GTF file should resemble the Ensembl format.
 
 ```bash
 --gtf '[path to GTF file]'
 ```
 
 ### `--bwa_index`
+
 Full path to an existing BWA index for your reference genome including the base name for the index.
 
 ```bash
 --bwa_index '[directory containing BWA index]/genome.fa'
 ```
 
 ### `--gene_bed`
+
 The full path to BED file for genome-wide gene intervals. This will be created from the GTF file if not specified.
 
 ```bash
 --gene_bed '[path to gene BED file]'
 ```
 
 ### `--tss_bed`
+
 The full path to BED file for genome-wide transcription start sites. This will be created from the gene BED file if not specified.
 
 ```bash
 --tss_bed '[path to tss BED file]'
 ```
 
 ### `--macs_gsize`
+
 [Effective genome size](https://github.com/taoliu/MACS#-g--gsize) parameter required by MACS2. These have been provided when `--genome` is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. For other genomes, if this parameter is not specified then the MACS2 peak-calling and differential analysis will be skipped.
 
 ```bash
 --macs_gsize 2.7e9
 ```
 
 ### `--blacklist`
+
 If provided, alignments that overlap with the regions in this file will be filtered out (see [ENCODE blacklists](https://sites.google.com/site/anshulkundaje/projects/blacklists)). The file should be in BED format. Blacklisted regions for *GRCh37*, *GRCh38*, *GRCm38*, *hg19*, *hg38*, *mm10* are bundled with the pipeline in the [`blacklists`](../assets/blacklists/) directory, and as such will be automatically used if any of those genomes are specified with the `--genome` parameter.
 
 ```bash
 --blacklist '[path to blacklisted regions]'
 ```
 
 ### `--save_reference`
+
 If the BWA index is generated by the pipeline use this parameter to save it to your results folder. These can then be used for future pipeline runs, reducing processing times.
 
 ### `--igenomes_ignore`
+
 Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
 
 ## Adapter trimming
+
 The pipeline accepts a number of parameters to change how the trimming is done, according to your data type.
 You can specify custom trimming parameters as follows:
 
@@ -336,41 +355,51 @@ You can specify custom trimming parameters as follows:
   * This enables the option Cutadapt `--nextseq-trim=3'CUTOFF` option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.
 
 ### `--skip_trimming`
+
 Skip the adapter trimming step. Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.
 
 ### `--save_trimmed`
+
 By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.
 
 ## Alignments
-narrow_peak
+
 ### `--keep_dups`
+
 Duplicate reads are not filtered from alignments.
 
 ### `--keep_multi_map`
+
 Reads mapping to multiple locations in the genome are not filtered from alignments.
 
 ### `--save_align_intermeds`
+
 By default, intermediate BAM files will not be saved. The final BAM files created after the appropriate filtering step are always saved to limit storage usage. Set to true to also save other intermediate BAM files.
 
 ## Peaks
 
 ### `--narrow_peak`
+
 MACS2 is run by default with the [`--broad`](https://github.com/taoliu/MACS#--broad) flag. Specify this flag to call peaks in narrowPeak mode.
 
 ### `--broad_cutoff`
+
 Specifies broad cut-off value for MACS2. Only used when `--narrow_peak` isnt specified (Default: `0.1`).
 
 ### `--min_reps_consensus`
+
 Number of biological replicates required from a given condition for a peak to contribute to a consensus peak . If you are confident you have good reproducibility amongst your replicates then you can increase the value of this parameter to create a "reproducible" set of consensus of peaks. For example, a value of 2 will mean peaks that have been called in at least 2 replicates will contribute to the consensus set of peaks, and as such peaks that are unique to a given replicate will be discarded.
 
 ```bash
 -- min_reps_consensus 1
 ```
 
 ### `--save_macs_pileup`
+
 Instruct MACS2 to create bedGraph files using the `-B --SPMR` parameters.
 
 ### `--skip_diff_analysis`
+
 Skip read counting and differential analysis step.
 
 ## Skipping QC steps
@@ -390,61 +419,77 @@ The following options make this easy:
 | `--skip_multiqc`          | Skip MultiQC                       |
 
 ## Job resources
+
 ### Automatic resubmission
+
 Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.
 
 ### Custom resource requests
+
 Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files hosted at [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
 
 If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack/).
 
 ## AWS Batch specific parameters
+
 Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration. Please use the `-awsbatch` profile and then specify all of the following parameters.
+
 ### `--awsqueue`
+
 The JobQueue that you intend to use on AWS Batch.
+
 ### `--awsregion`
+
 The AWS region to run your job in. Default is set to `eu-west-1` but can be adjusted to your needs.
 
 Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a S3 storage bucket of your choice - you'll get an error message notifying you if you didn't.
 
 ## Other command line parameters
 
 ### `--outdir`
+
 The output directory where the results will be saved.
 
 ### `--email`
+
 Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
 
 ### `--email_on_fail`
+
 This works exactly as with `--email`, except emails are only sent if the workflow is not successful.
 
 ### `--max_multiqc_email_size`
-Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: `25MB`).
+
+Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: `25MB`).
 
 ### `-name`
+
 Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
 
 This is used in the MultiQC report (if not default) and in the summary HTML / e-mail (always).
 
 **NB:** Single hyphen (core Nextflow option)
 
 ### `-resume`
+
 Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.
 
 You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
 
 **NB:** Single hyphen (core Nextflow option)
 
 ### `-c`
+
 Specify the path to a specific config file (this is a core NextFlow command).
 
 **NB:** Single hyphen (core Nextflow option)
 
 Note - you can use this to override pipeline defaults.
 
 ### `--custom_config_version`
+
 Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.
 
 ```bash
@@ -453,6 +498,7 @@ Provide git commit id for custom Institutional configs hosted at `nf-core/config
 ```
 
 ### `--custom_config_base`
+
 If you're running offline, nextflow will not be able to fetch the institutional config files
 from the internet. If you don't need them, then this is not a problem. If you do need them,
 you should download the files from the repo and tell nextflow where to find them with the
@@ -473,22 +519,28 @@ nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs
 > files + singularity containers + institutional configs in one go for you, to make this process easier.
 
 ### `--max_memory`
+
 Use to set a top-limit for the default memory requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_memory '8.GB'`
 
 ### `--max_time`
+
 Use to set a top-limit for the default time requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_time '2.h'`
 
 ### `--max_cpus`
+
 Use to set a top-limit for the default CPU requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_cpus 1`
 
 ### `--plaintext_email`
+
 Set to receive plain-text e-mails instead of HTML formatted.
 
 ### `--monochrome_logs`
+
 Set to disable colourful command line output and live life in monochrome.
 
 ### `--multiqc_config`
+
 Specify a path to a custom MultiQC configuration file.