Find and replace NGI-MethylSeq > nf-core/MethylSeq

CHANGELOG.md

@@ -1,6 +1,8 @@
 # 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/)
+* Refactoring multi-core parameters for Bismark alignment and methylation extraction
 * Fix for iGenomes base path in configs
 
 ## [v0.3.1](https://github.com/SciLifeLab/NGI-MethylSeq/releases/tag/0.3.1) - 2017-09-05

Dockerfile

@@ -2,7 +2,7 @@
 FROM openjdk:8u121
 
 LABEL authors="[email protected],[email protected]" \
-    description="Docker image containing all requirements for NGI-MethylSeq pipeline"
+    description="Docker image containing all requirements for nf-core/MethylSeq pipeline"
 
 # Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
 RUN apt-get update && \

Dockerfile-bwa

@@ -2,7 +2,7 @@
 FROM openjdk:8u121
 
 LABEL authors="[email protected],[email protected]" \
-    description="Docker image containing all requirements for NGI-MethylSeq pipeline"
+    description="Docker image containing all requirements for nf-core/MethylSeq pipeline"
 
 # Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
 RUN apt-get update && \

README.md

@@ -1,37 +1,32 @@
-# ![NGI-MethylSeq](docs/images/NGI-MethylSeq_logo.png)
+# ![nf-core/MethylSeq](docs/images/MethylSeq_logo.png)
 
-[![Build Status](https://travis-ci.org/SciLifeLab/NGI-MethylSeq.svg?branch=master)](https://travis-ci.org/SciLifeLab/NGI-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
 
-NGI-MethylSeq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the [National Genomics Infastructure](https://ngisweden.scilifelab.se/) at [SciLifeLab Stockholm](https://www.scilifelab.se/platforms/ngi/), Sweden.
+`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.
 
 ### Choice of workflows
 
 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.
 
-### Hardware requirements
-
-This pipeline is primarily used with a SLURM cluster on the Swedish [UPPMAX systems](https://www.uppmax.uu.se). However, the pipeline should be able to run on any system that Nextflow supports. We have done some limited testing using Docker and AWS, and the pipeline comes with some configuration for these systems. See the [installation docs](docs/installation.md) for more information.
-
 ### Documentation
-The NGI-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)
 3. [Output and how to interpret the results](docs/output.md)
 
-If you're interested in running the pipeline in the cloud, please read the docs about using our pipeline with Amazon Web Services on the [NGI-RNAseq pipeline](https://github.com/SciLifeLab/NGI-RNAseq/blob/master/docs/amazon_web_services.md) (the instructions should work with this pipeline as well).
 
 ### Credits
 These scripts were written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. Written by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn).
 
 ---
 
-[![SciLifeLab](https://raw.githubusercontent.com/SciLifeLab/NGI-MethylSeq/master/docs/images/SciLifeLab_logo.png)](http://www.scilifelab.se/)
-[![National Genomics Infrastructure](https://raw.githubusercontent.com/SciLifeLab/NGI-MethylSeq/master/docs/images/NGI_logo.png)](https://ngisweden.scilifelab.se/)
+[![SciLifeLab](https://raw.githubusercontent.com/nf-core/MethylSeq/master/docs/images/SciLifeLab_logo.png)](http://www.scilifelab.se/)
+[![National Genomics Infrastructure](https://raw.githubusercontent.com/nf-core/MethylSeq/master/docs/images/NGI_logo.png)](https://ngisweden.scilifelab.se/)
 
 ---

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="NGI-MethylSeq: a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.">
-  <title>NGI-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>NGI-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;">
-        NGI-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;">NGI-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>NGI-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/SciLifeLab/NGI-MethylSeq">https://github.com/SciLifeLab/NGI-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 @@
 =================================================
- NGI-MethylSeq: Bisulfite-Seq Best Practice v${version}
+ nf-core/MethylSeq: Bisulfite-Seq Best Practice v${version}
 =================================================
 Run Name: $runName
 
 <% if (success){
-    out << "## NGI-MethylSeq execution completed successfully! ##"
+    out << "## nf-core/MethylSeq execution completed successfully! ##"
 } else {
     out << """####################################################
-## NGI-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") %>
 
 --
-NGI-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/SciLifeLab/NGI-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="NGI-MethylSeq_logo.png"
+Content-Type: image/png;name="MethylSeq_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <ngimethylseqlogo>
-Content-Disposition: inline; filename="NGI-MethylSeq_logo.png"
+Content-Disposition: inline; filename="MethylSeq_logo.png"
 
-<% out << new File("$baseDir/assets/NGI-MethylSeq_logo.png").
+<% out << new File("$baseDir/assets/MethylSeq_logo.png").
   bytes.
   encodeBase64().
   toString().

bin/scrape_software_versions.py

@@ -4,7 +4,7 @@
 import re
 
 regexes = {
-    'NGI-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+)"],
@@ -20,7 +20,7 @@
     'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
 }
 results = OrderedDict()
-results['NGI-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>'
@@ -46,8 +46,8 @@
 # Dump to YAML
 print ('''
 id: 'software_versions'
-section_name: 'NGI-MethylSeq Software Versions'
-section_href: 'https://github.com/SciLifeLab/NGI-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: |

bismark.nf

@@ -7,7 +7,7 @@ vim: syntax=groovy
 ========================================================================================
  New Methylation (BS-Seq) Best Practice Analysis Pipeline. Started June 2016.
  #### Homepage / Documentation
- https://github.com/SciLifeLab/NGI-MethylSeq
+ https://github.com/nf-core/MethylSeq
  #### Authors
  Phil Ewels <[email protected]>
 ----------------------------------------------------------------------------------------
@@ -150,7 +150,7 @@ Channel
     .into { read_files_fastqc; read_files_trimming }
 
 log.info "=================================================="
-log.info " NGI-MethylSeq : Bisulfite-Seq Best Practice v${version}"
+log.info " nf-core/MethylSeq : Bisulfite-Seq Best Practice v${version}"
 log.info "=================================================="
 def summary = [:]
 summary['Run Name']       = custom_runName ?: workflow.runName
@@ -603,9 +603,9 @@ process multiqc {
 workflow.onComplete {
 
     // Set up the e-mail variables
-    def subject = "[NGI-MethylSeq] Successful: $workflow.runName"
+    def subject = "[nf-core/MethylSeq] Successful: $workflow.runName"
     if(!workflow.success){
-      subject = "[NGI-MethylSeq] FAILED: $workflow.runName"
+      subject = "[nf-core/MethylSeq] FAILED: $workflow.runName"
     }
     def email_fields = [:]
     email_fields['version'] = version
@@ -654,16 +654,16 @@ 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 "[NGI-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 "[NGI-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("$baseDir/assets/NGI-MethylSeq_logo.png").bytes.encodeBase64().toString()
+    ngimethylseqlogo = new File("$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")
@@ -680,7 +680,7 @@ workflow.onComplete {
     def output_tf = new File( output_d, "pipeline_report.txt" )
     output_tf.withWriter { w -> w << email_txt }
 
-    log.info "[NGI-MethylSeq] Pipeline Complete"
+    log.info "[nf-core/MethylSeq] Pipeline Complete"
 
     if(!workflow.success){
         if( workflow.profile == 'standard'){

bwa-meth.nf

@@ -7,7 +7,7 @@ vim: syntax=groovy
 ========================================================================================
  Methylation (BS-Seq) Analysis Pipeline using bwa-meth. Started November 2016.
  #### Homepage / Documentation
- https://github.com/SciLifeLab/NGI-MethylSeq
+ https://github.com/nf-core/MethylSeq
  #### Authors
  Phil Ewels <[email protected]>
 ----------------------------------------------------------------------------------------
@@ -94,7 +94,7 @@ if(params.pbat){
 def single
 
 log.info "==================================================="
-log.info " NGI-MethylSeq : Bisulfite-Seq BWA-Meth v${version}"
+log.info " nf-core/MethylSeq : Bisulfite-Seq BWA-Meth v${version}"
 log.info "==================================================="
 log.info "Reads          : ${params.reads}"
 log.info "Genome         : ${params.genome}"

conf/multiqc_config.yaml

@@ -1,7 +1,7 @@
 report_comment: >
-    This report has been generated by the <a href="https://github.com/SciLifeLab/NGI-MethylSeq" target="_blank">NGI-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/SciLifeLab/NGI-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:

docs/README.md

@@ -1,11 +1,11 @@
-# NGI-MethylSeq Results
+# nf-core/MethylSeq Results
 
-The NGI-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 NGI-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.