From df885d9d1b01132a85b5b59796a6ed3e268caad3 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 12 Mar 2018 17:05:10 +0100 Subject: [PATCH] Drop capitals: MethylSeq to methylseq --- CHANGELOG.md | 2 +- Dockerfile | 2 +- README.md | 10 +++++----- assets/email_template.html | 14 +++++++------- assets/email_template.txt | 10 +++++----- assets/sendmail_template.txt | 6 +++--- bin/scrape_software_versions.py | 8 ++++---- conf/multiqc_config.yaml | 4 ++-- conf/test.config | 2 +- docs/README.md | 6 +++--- .../{MethylSeq_logo.ai => methylseq_logo.ai} | 0 .../{MethylSeq_logo.png => methylseq_logo.png} | Bin docs/installation.md | 14 +++++++------- docs/output.md | 10 +++++----- docs/usage.md | 6 +++--- main.nf | 16 ++++++++-------- nextflow.config | 2 +- 17 files changed, 56 insertions(+), 56 deletions(-) rename docs/images/{MethylSeq_logo.ai => methylseq_logo.ai} (100%) rename docs/images/{MethylSeq_logo.png => methylseq_logo.png} (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 79a919f..d9b4b9b 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/Dockerfile b/Dockerfile index e7456a6..0127bcc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ FROM continuumio/miniconda MAINTAINER Phil Ewels LABEL authors="phil.ewels@scilifelab.se" \ - 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 diff --git a/README.md b/README.md index a454b25..7b7cbb5 100644 --- a/README.md +++ b/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. diff --git a/assets/email_template.html b/assets/email_template.html index 5bcf3eb..a7d3406 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,27 +4,27 @@ - - nf-core/MethylSeq Pipeline Report + + nf-core/methylseq Pipeline Report
-

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! + 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:

${errorReport}
@@ -44,9 +44,9 @@

Pipeline Configuration:
-

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

diff --git a/assets/email_template.txt b/assets/email_template.txt index 22019ac..4eb4bab 100644 --- a/assets/email_template.txt +++ b/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 diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index ecf8c2a..21c0375 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8 $email_html --ngimimeboundary -Content-Type: image/png;name="MethylSeq_logo.png" +Content-Type: image/png;name="methylseq_logo.png" Content-Transfer-Encoding: base64 Content-ID: -Content-Disposition: inline; filename="MethylSeq_logo.png" +Content-Disposition: inline; filename="methylseq_logo.png" -<% out << new File("$baseDir/assets/MethylSeq_logo.png"). +<% out << new File("$baseDir/assets/methylseq_logo.png"). bytes. encodeBase64(). toString(). diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 9c2509c..68483a5 100755 --- a/bin/scrape_software_versions.py +++ b/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'] = 'N/A' +results['nf-core/methylseq'] = 'N/A' results['Nextflow'] = 'N/A' results['Bismark genomePrep'] = 'N/A' results['FastQC'] = 'N/A' @@ -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: | diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml index 4289d6a..944545e 100644 --- a/conf/multiqc_config.yaml +++ b/conf/multiqc_config.yaml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/MethylSeq + This report has been generated by the nf-core/methylseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. swedac_accredited: false report_section_order: software_versions: diff --git a/conf/test.config b/conf/test.config index 9ad156d..d51efce 100644 --- a/conf/test.config +++ b/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 diff --git a/docs/README.md b/docs/README.md index 90a944a..0a42057 100644 --- a/docs/README.md +++ b/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. diff --git a/docs/images/MethylSeq_logo.ai b/docs/images/methylseq_logo.ai similarity index 100% rename from docs/images/MethylSeq_logo.ai rename to docs/images/methylseq_logo.ai diff --git a/docs/images/MethylSeq_logo.png b/docs/images/methylseq_logo.png similarity index 100% rename from docs/images/MethylSeq_logo.png rename to docs/images/methylseq_logo.png diff --git a/docs/installation.md b/docs/installation.md index aad11c6..8a98c54 100644 --- a/docs/installation.md +++ b/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. diff --git a/docs/output.md b/docs/output.md index a111c6f..ded6cf0 100644 --- a/docs/output.md +++ b/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. diff --git a/docs/usage.md b/docs/usage.md index 242c81a..7770fa8 100644 --- a/docs/usage.md +++ b/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. diff --git a/main.nf b/main.nf index 0cca7bc..0af5658 100644 --- a/main.nf +++ b/main.nf @@ -7,7 +7,7 @@ vim: syntax=groovy ======================================================================================== New Methylation (BS-Seq) Best Practice Analysis Pipeline. Started June 2016. #### Homepage / Documentation - https://github.com/nf-core/MethylSeq + https://github.com/nf-core/methylseq #### Authors Phil Ewels ---------------------------------------------------------------------------------------- @@ -145,7 +145,7 @@ Channel .into { read_files_fastqc; read_files_trimming } log.info "==================================================" -log.info " nf-core/MethylSeq : Bisulfite-Seq Best Practice v${params.version}" +log.info " nf-core/methylseq : Bisulfite-Seq Best Practice v${params.version}" log.info "==================================================" def summary = [:] summary['Run Name'] = custom_runName ?: workflow.runName @@ -796,9 +796,9 @@ process multiqc { workflow.onComplete { // Set up the e-mail variables - def subject = "[nf-core/MethylSeq] Successful: $workflow.runName" + def subject = "[nf-core/methylseq] Successful: $workflow.runName" if(!workflow.success){ - subject = "[nf-core/MethylSeq] FAILED: $workflow.runName" + subject = "[nf-core/methylseq] FAILED: $workflow.runName" } def email_fields = [:] email_fields['version'] = params.version @@ -847,16 +847,16 @@ workflow.onComplete { if( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "[nf-core/MethylSeq] Sent summary e-mail to $params.email (sendmail)" + log.info "[nf-core/methylseq] Sent summary e-mail to $params.email (sendmail)" } catch (all) { // Catch failures and try with plaintext [ 'mail', '-s', subject, params.email ].execute() << email_txt - log.info "[nf-core/MethylSeq] Sent summary e-mail to $params.email (mail)" + log.info "[nf-core/methylseq] Sent summary e-mail to $params.email (mail)" } } // Switch the embedded MIME images with base64 encoded src - ngimethylseqlogo = new File("$baseDir/assets/MethylSeq_logo.png").bytes.encodeBase64().toString() + ngimethylseqlogo = new File("$baseDir/assets/methylseq_logo.png").bytes.encodeBase64().toString() scilifelablogo = new File("$baseDir/assets/SciLifeLab_logo.png").bytes.encodeBase64().toString() ngilogo = new File("$baseDir/assets/NGI_logo.png").bytes.encodeBase64().toString() email_html = email_html.replaceAll(~/cid:ngimethylseqlogo/, "data:image/png;base64,$ngimethylseqlogo") @@ -873,7 +873,7 @@ workflow.onComplete { def output_tf = new File( output_d, "pipeline_report.txt" ) output_tf.withWriter { w -> w << email_txt } - log.info "[nf-core/MethylSeq] Pipeline Complete" + log.info "[nf-core/methylseq] Pipeline Complete" if(!workflow.success){ if( workflow.profile == 'standard'){ diff --git a/nextflow.config b/nextflow.config index 49aeeee..9acfbe9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -97,7 +97,7 @@ dag { } manifest { - homePage = 'https://github.com/nf-core/MethylSeq' + homePage = 'https://github.com/nf-core/methylseq' description = 'Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.' mainScript = 'main.nf' }