Drop capitals: MethylSeq to methylseq

CHANGELOG.md

@@ -1,7 +1,7 @@
 # NGI-MethylSeq
 
 ## v0.4dev
-* Renaming and moving [SciLifeLab/NGI-MethylSeq](https://github.com/SciLifeLab/NGI-MethylSeq/) to [nf-core/MethylSeq](https://github.com/nf-core/MethylSeq/)
+* Renaming and moving [SciLifeLab/NGI-MethylSeq](https://github.com/SciLifeLab/NGI-MethylSeq/) to [nf-core/methylseq](https://github.com/nf-core/methylseq/)
 * Refactoring multi-core parameters for Bismark alignment and methylation extraction
 * Fix for iGenomes base path in configs
 

Dockerfile

@@ -1,7 +1,7 @@
 FROM continuumio/miniconda
 MAINTAINER Phil Ewels <[email protected]>
 LABEL authors="[email protected]" \
-    description="Docker image containing all requirements for the nf-core/MethylSeq pipeline"
+    description="Docker image containing all requirements for the nf-core/methylseq pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml

README.md

@@ -1,11 +1,11 @@
-# ![nf-core/MethylSeq](docs/images/MethylSeq_logo.png)
+# ![nf-core/methylseq](docs/images/methylseq_logo.png)
 
-[![Build Status](https://travis-ci.org/nf-core/MethylSeq.svg?branch=master)](https://travis-ci.org/nf-core/MethylSeq)
+[![Build Status](https://travis-ci.org/nf-core/methylseq.svg?branch=master)](https://travis-ci.org/nf-core/methylseq)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.25.1-brightgreen.svg)](https://www.nextflow.io/)
 
 ### Introduction
 
-**nf-core/MethylSeq** is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis.
+**nf-core/methylseq** is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis.
 
 The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
 
@@ -14,7 +14,7 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
 There are two separate workflows contained in this repository - one using [Bismark](https://github.com/FelixKrueger/Bismark) and one using [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel). The Bismark pipeline is being actively developed and maintained, the bwa-meth workflow is not _(currently)_. The Nextflow manifest specifies the Bismark pipeline as the default workflow, so the bwa-meth script will be ignored unless explicitly run.
 
 ### Documentation
-The nf-core/MethylSeq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
+The nf-core/methylseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
 1. [Installation and configuration](docs/installation.md)
 2. [Running the pipeline](docs/usage.md)
@@ -32,7 +32,7 @@ These scripts were originally written for use at the [National Genomics Infrastr
 
 
 ### Participating Institutes
-**nf-core/MethylSeq** is used by a number of core sequencing and bioinformatics facilities. Some of these are listed below. If you use this pipeline too, please let us know in an issue and we will add you to the list.
+**nf-core/methylseq** is used by a number of core sequencing and bioinformatics facilities. Some of these are listed below. If you use this pipeline too, please let us know in an issue and we will add you to the list.
 
 <table>
   <tr>

assets/email_template.html

@@ -4,27 +4,27 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/MethylSeq: a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.">
-  <title>nf-core/MethylSeq Pipeline Report</title>
+  <meta name="description" content="nf-core/methylseq: a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.">
+  <title>nf-core/methylseq Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
 <img src="cid:ngimethylseqlogo">
 
-<h1>nf-core/MethylSeq: Bisulfite-Seq Best Practice v${version}</h1>
+<h1>nf-core/methylseq: Bisulfite-Seq Best Practice v${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (success){
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nf-core/MethylSeq execution completed successfully!
+        nf-core/methylseq execution completed successfully!
     </div>
     """
 } else {
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf-core/MethylSeq execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">nf-core/methylseq execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -44,9 +44,9 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>nf-core/MethylSeq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.</p>
+<p>nf-core/methylseq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.</p>
 <p>The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.</p>
-<p>For more information, please see the pipeline homepage: <a href="https://github.com/nf-core/MethylSeq">https://github.com/nf-core/MethylSeq</a></p>
+<p>For more information, please see the pipeline homepage: <a href="https://github.com/nf-core/methylseq">https://github.com/nf-core/methylseq</a></p>
 
 <hr style="height: 3px; padding: 0; margin: 24px 0; background-color: #e1e4e8; border: 0;">
 

assets/email_template.txt

@@ -1,13 +1,13 @@
 =================================================
- nf-core/MethylSeq: Bisulfite-Seq Best Practice v${version}
+ nf-core/methylseq: Bisulfite-Seq Best Practice v${version}
 =================================================
 Run Name: $runName
 
 <% if (success){
-    out << "## nf-core/MethylSeq execution completed successfully! ##"
+    out << "## nf-core/methylseq execution completed successfully! ##"
 } else {
     out << """####################################################
-## nf-core/MethylSeq execution completed unsuccessfully! ##
+## nf-core/methylseq execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -28,7 +28,7 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-nf-core/MethylSeq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.
+nf-core/methylseq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.
 The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
-For more information, please see the pipeline homepage: https://github.com/nf-core/MethylSeq
+For more information, please see the pipeline homepage: https://github.com/nf-core/methylseq
 

assets/sendmail_template.txt

@@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --ngimimeboundary
-Content-Type: image/png;name="MethylSeq_logo.png"
+Content-Type: image/png;name="methylseq_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <ngimethylseqlogo>
-Content-Disposition: inline; filename="MethylSeq_logo.png"
+Content-Disposition: inline; filename="methylseq_logo.png"
 
-<% out << new File("$baseDir/assets/MethylSeq_logo.png").
+<% out << new File("$baseDir/assets/methylseq_logo.png").
   bytes.
   encodeBase64().
   toString().

bin/scrape_software_versions.py

@@ -4,7 +4,7 @@
 import re
 
 regexes = {
-    'nf-core/MethylSeq': ['v_ngi_methylseq.txt', r"(\S+)"],
+    'nf-core/methylseq': ['v_ngi_methylseq.txt', r"(\S+)"],
     'Nextflow': ['v_nextflow.txt', r"(\S+)"],
     'Bismark genomePrep': ['v_bismark_genome_preparation.txt', r"Bismark Genome Preparation Version: v(\S+)"],
     'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
@@ -24,7 +24,7 @@
     'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
 }
 results = OrderedDict()
-results['nf-core/MethylSeq'] = '<span style="color:#999999;\">N/A</span>'
+results['nf-core/methylseq'] = '<span style="color:#999999;\">N/A</span>'
 results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
 results['Bismark genomePrep'] = '<span style="color:#999999;\">N/A</span>'
 results['FastQC'] = '<span style="color:#999999;\">N/A</span>'
@@ -59,8 +59,8 @@
 # Dump to YAML
 print ('''
 id: 'software_versions'
-section_name: 'nf-core/MethylSeq Software Versions'
-section_href: 'https://github.com/nf-core/MethylSeq'
+section_name: 'nf-core/methylseq Software Versions'
+section_href: 'https://github.com/nf-core/methylseq'
 plot_type: 'html'
 description: 'are collected at run time from the software output.'
 data: |

conf/multiqc_config.yaml

@@ -1,7 +1,7 @@
 report_comment: >
-    This report has been generated by the <a href="https://github.com/nf-core/MethylSeq" target="_blank">nf-core/MethylSeq</a>
+    This report has been generated by the <a href="https://github.com/nf-core/methylseq" target="_blank">nf-core/methylseq</a>
     analysis pipeline. For information about how to interpret these results, please see the
-    <a href="https://github.com/nf-core/MethylSeq/blob/master/docs/README.md" target="_blank">documentation</a>.
+    <a href="https://github.com/nf-core/methylseq/blob/master/docs/README.md" target="_blank">documentation</a>.
 swedac_accredited: false
 report_section_order:
     software_versions:

conf/test.config

@@ -6,7 +6,7 @@ vim: syntax=groovy
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/MethylSeq -profile test
+ *   nextflow run nf-core/methylseq -profile test
  */
 
 // resume: true

docs/README.md

@@ -1,11 +1,11 @@
-# nf-core/MethylSeq Results
+# nf-core/methylseq Results
 
-The nf-core/MethylSeq documentation is split into a few different files:
+The nf-core/methylseq documentation is split into a few different files:
 
 * [`installation.md`](installation.md)
   * Pipeline installation and configuration instructions
 * [`usage.md`](usage.md)
-  * Instructions on how to run the nf-core/MethylSeq pipeline
+  * Instructions on how to run the nf-core/methylseq pipeline
 * [`output.md`](output.md)
   * Document describing all of the results produced by the pipeline, and how to interpret them.
 

docs/installation.md

@@ -1,6 +1,6 @@
-# nf-core/MethylSeq Installation
+# nf-core/methylseq Installation
 
-To start using the nf-core/MethylSeq pipeline, there are three steps described below:
+To start using the nf-core/methylseq pipeline, there are three steps described below:
 
 1. [Install Nextflow](#1-install-nextflow)
 2. [Install the pipeline](#2-install-the-pipeline)
@@ -29,14 +29,14 @@ mv nextflow ~/bin
 See [nextflow.io](https://www.nextflow.io/) and [NGI-NextflowDocs](https://github.com/SciLifeLab/NGI-NextflowDocs) for further instructions on how to install and configure Nextflow.
 
 ## 2) Install the Pipeline
-This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if `nf-core/MethylSeq` is specified as the pipeline name.
+This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if `nf-core/methylseq` is specified as the pipeline name.
 
 If you prefer, you can download the files yourself from GitHub and run them directly:
 
 ```bash
-git clone https://github.com/nf-core/MethylSeq.git
-nextflow run nf-core/MethylSeq/bismark.nf
-nextflow run nf-core/MethylSeq/bwa-meth.nf # Alternative bwa-meth pipeline
+git clone https://github.com/nf-core/methylseq.git
+nextflow run nf-core/methylseq/bismark.nf
+nextflow run nf-core/methylseq/bwa-meth.nf # Alternative bwa-meth pipeline
 ```
 
 ## 3) Pipeline Configuration
@@ -110,7 +110,7 @@ process {
 ```
 
 ### Reference Genomes
-The nf-core/MethylSeq pipeline needs a reference genome for read alignment. Support for many common genomes is built in if running on UPPMAX or AWS, by using [illumina iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).
+The nf-core/methylseq pipeline needs a reference genome for read alignment. Support for many common genomes is built in if running on UPPMAX or AWS, by using [illumina iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).
 
 If you don't want to use the illumina iGenomes you can supply either a Bismark reference or a FASTA file. If a Bismark reference is specified, the pipeline won't have to generate it and will be finished quite a bit faster. If a FASTA file is supplied then the Bismark reference will be built when the pipeline starts. Use the command line option `--saveReference` to keep the generated references so that they can be added to your config and used again in the future. Use  `--bismark_index` or `--fasta` to specify the paths to the reference.
 

docs/output.md

@@ -1,10 +1,10 @@
-# nf-core/MethylSeq Output
+# nf-core/methylseq Output
 
-nf-core/MethylSeq is the new RNA-seq Best Practice pipeline used by the [National Genomics Infrastructure](https://ngisweden.scilifelab.se/) at [SciLifeLab](https://www.scilifelab.se/platforms/ngi/) in Stockholm, Sweden.
+nf-core/methylseq is the new RNA-seq Best Practice pipeline used by the [National Genomics Infrastructure](https://ngisweden.scilifelab.se/) at [SciLifeLab](https://www.scilifelab.se/platforms/ngi/) in Stockholm, Sweden.
 
 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.
 
-Note that nf-core/MethylSeq contains two workflows - one for Bismark, one for bwa-meth. This document describes the output from the default Bismark workflow.
+Note that nf-core/methylseq contains two workflows - one for Bismark, one for bwa-meth. This document describes the output from the default Bismark workflow.
 
 ## Pipeline overview
 The pipeline is built using [Nextflow](https://www.nextflow.io/)
@@ -36,7 +36,7 @@ For further reading and documentation see the [FastQC help](http://www.bioinform
   * zip file containing the FastQC report, tab-delimited data file and plot images
 
 ## TrimGalore
-The nf-core/MethylSeq BP 2.0 pipeline uses [TrimGalore](http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for removal of adapter contamination and trimming of low quality regions. TrimGalore uses [Cutadapt](https://github.com/marcelm/cutadapt) for adapter trimming and runs FastQC after it finishes.
+The nf-core/methylseq BP 2.0 pipeline uses [TrimGalore](http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for removal of adapter contamination and trimming of low quality regions. TrimGalore uses [Cutadapt](https://github.com/marcelm/cutadapt) for adapter trimming and runs FastQC after it finishes.
 
 MultiQC reports the percentage of bases removed by TrimGalore in the _General Statistics_ table, along with a line plot showing where reads were trimmed.
 
@@ -55,7 +55,7 @@ Contains FastQ files with quality and adapter trimmed reads for each sample, alo
 Single-end data will have slightly different file names and only one FastQ file per sample.
 
 ## Bismark
-The default nf-core/MethylSeq workflow uses [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) to process raw sequencing reads into cytosine methylation calls.
+The default nf-core/methylseq workflow uses [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) to process raw sequencing reads into cytosine methylation calls.
 
 ### Alignment
 Bismark converts all Cytosines to Thymine _in-silico_ and then aligns against a three-letter reference genome. It produces a BAM file of genomic alignments.

docs/usage.md

@@ -1,8 +1,8 @@
-# nf-core/MethylSeq Usage
+# nf-core/methylseq Usage
 
 ## Bismark and bwa-meth workflow
 
-The nf-core/MethylSeq package is actually two pipelines in one. The default (and most polished) workflow uses [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) for processing and can be found in `bismark.nf`. Unless specified otherwise, nf-core/MethylSeq will run this pipeline.
+The nf-core/methylseq package is actually two pipelines in one. The default (and most polished) workflow uses [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) for processing and can be found in `bismark.nf`. Unless specified otherwise, nf-core/methylseq will run this pipeline.
 
 The second included workflow uses [BWA-Meth](https://github.com/brentp/bwa-meth) and [MethylDackyl](https://github.com/dpryan79/methyldackel) instead of Bismark and can be found in `bwa-meth.nf`. To run this workflow, you must download the repository files and explicitly call `nextflow run /path/to/files/bwa-meth.nf`. Note that this workflow has not been tested to the same extent and may have bugs.
 
@@ -12,7 +12,7 @@ All of the documentation refers to the Bismark workflow at this stage, though mo
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/MethylSeq --genome GRCh37 --reads '*_R{1,2}.fastq.gz' -profile docker
+nextflow run nf-core/methylseq --genome GRCh37 --reads '*_R{1,2}.fastq.gz' -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile (Swedish UPPMAX users use `-profile uppmax`). See below for more information about profiles.