nf-core · ewels · Mar 29, 2018 · Mar 29, 2018 · Mar 29, 2018 · Apr 4, 2018
diff --git a/.travis.yml b/.travis.yml
@@ -10,19 +10,19 @@ matrix:
   fast_finish: true
 
 env:
-  - FLAGS="-a star" INST=nt NXF_VER=0.27.6
-  - FLAGS="-a star" INST=nt
-  - FLAGS="-a star -s" INST=nts SGT_VER=2.4.5
-  - FLAGS="-a hisat2" INST=nt NXF_VER=0.27.6
-  - FLAGS="-a hisat2" INST=nt
-  - FLAGS="-a hisat2 -s" INST=nts SGT_VER=2.4.5
+  - T=nt  FL="-a star" NXF_VER=0.27.6
+  - T=nt  FL="-a star"
+  - T=nts FL="-a star -s"
+  - T=nt  FL="-a hisat2" NXF_VER=0.27.6
+  - T=nt  FL="-a hisat2"
+  - T=nts FL="-a hisat2 -s"
 
-install: # Install Singularity if needed
-  - "./tests/install.sh $INST"
+install:
+  - "./tests/install.sh $T"
   - "cd ${TRAVIS_BUILD_DIR}/tests/"
 
 script:
   - "nf-core lint ${TRAVIS_BUILD_DIR}"
-  - "travis_wait 30 ./run_test.sh ${FLAGS} -b"
-  - "travis_wait 30 ./run_test.sh ${FLAGS}"
-  - "tree --dirsfirst results/"
+  - "./run_test.sh ${FL} -b"
+  - "./run_test.sh ${FL}"
+  - "find results/" # Print results files
diff --git a/Dockerfile b/Dockerfile
@@ -1,10 +1,8 @@
-FROM continuumio/miniconda
+FROM nfcore/base
 MAINTAINER Phil Ewels <phil.ewels@scilifelab.se>
 LABEL authors="phil.ewels@scilifelab.se" \
     description="Docker image containing all requirements for the nfcore/RNAseq pipeline"
 
 COPY environment.yml /
-RUN conda update -n base conda && \
-    conda env create -f /environment.yml && \
-    conda clean -a
+RUN conda env create -f /environment.yml && conda clean -a
 ENV PATH /opt/conda/envs/nfcore-rnaseq/bin:$PATH
diff --git a/assets/NGI-RNAseq_logo.png b/assets/NGI-RNAseq_logo.png
diff --git a/assets/email_template.html b/assets/email_template.html
@@ -13,7 +13,7 @@
 
 <img src="cid:ngirnaseqlogo">
 
-<h1>nfcore/RNAseq: RNA-Seq Best Practice v${version}</h1>
+<h1>nfcore/RNAseq: version ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){

diff --git a/assets/email_template.txt b/assets/email_template.txt
@@ -1,5 +1,5 @@
 ========================================
- nfcore/RNAseq: RNA-Seq Best Practice v${version}
+ nfcore/RNAseq: version ${version}
 ========================================
 Run Name: $runName
 

diff --git a/assets/nfcore-rnaseq_logo.png b/assets/nfcore-rnaseq_logo.png
diff --git a/conf/aws.config b/conf/aws.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file for Amazon Web Services
  * -------------------------------------------------

diff --git a/conf/base.config b/conf/base.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow base config file
  * -------------------------------------------------

diff --git a/conf/binac.config b/conf/binac.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * ----------------------------------------------------------------------------
  *  Nextflow config file for use with Singularity on BINAC cluster in Tuebingen
  * ----------------------------------------------------------------------------

diff --git a/conf/cfc.config b/conf/cfc.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------------------
  *  Nextflow config file for use with Singularity on CFC at QBIC
  * -------------------------------------------------------------

diff --git a/conf/docker.config b/conf/docker.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file for use with Docker
  * -------------------------------------------------

diff --git a/conf/hebbe.config b/conf/hebbe.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Gothenburg Hebbe Cluster config file
  * -------------------------------------------------

diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file for iGenomes paths
  * -------------------------------------------------

diff --git a/conf/singularity.config b/conf/singularity.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file for use with Singularity
  * -------------------------------------------------

diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file for UPPMAX (milou / irma)
  * -------------------------------------------------

diff --git a/conf/uppmax-modules.config b/conf/uppmax-modules.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file with environment modules for UPPMAX (milou / irma)
  * -------------------------------------------------

diff --git a/conf/uppmax.config b/conf/uppmax.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file for UPPMAX (milou / irma)
  * -------------------------------------------------

diff --git a/docs/output.md b/docs/output.md
@@ -1,8 +1,8 @@
 # nfcore/RNAseq Output
 
-nfcore/RNAseq 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.
+nfcore/RNAseq is an RNA-seq analysis pipeline. This document describes the output produced by the pipeline.
 
-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.
+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/)
@@ -43,7 +43,7 @@ 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 nfcore/RNAseq 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 nfcore/RNAseq 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.
 

diff --git a/main.nf b/main.nf
@@ -1,26 +1,22 @@
 #!/usr/bin/env nextflow
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
-========================================================================================
-               N G I - R N A S E Q    B E S T    P R A C T I C E
-========================================================================================
- New RNA-Seq Best Practice Analysis Pipeline. Started March 2016.
+===============================================================
+ nf-core/RNAseq
+===============================================================
+ RNA-Seq Analysis Pipeline. Started March 2016.
  #### Homepage / Documentation
  https://github.com/nf-core/RNAseq
  #### Authors
  Phil Ewels @ewels <phil.ewels@scilifelab.se>
  Rickard Hammarén @Hammarn  <rickard.hammaren@scilifelab.se>
- Docker and AWS integration by
- Denis Moreno @Galithil <denis.moreno@scilifelab.se>
-----------------------------------------------------------------------------------------
+---------------------------------------------------------------
 */
 
 def helpMessage() {
     log.info"""
-    =========================================
-     nfcore/RNAseq : RNA-Seq Best Practice v${params.version}
-    =========================================
+    ===================================
+     nfcore/RNAseq  ~  version ${params.version}
+    ===================================
     Usage:
 
     The typical command for running the pipeline is as follows:
@@ -199,9 +195,9 @@ Channel
 
 
 // Header log info
-log.info "========================================="
-log.info " nfcore/RNAseq : RNA-Seq Best Practice v${params.version}"
-log.info "========================================="
+log.info "==================================="
+log.info " nfcore/RNAseq  ~  version ${params.version}"
+log.info "==================================="
 def summary = [:]
 summary['Run Name']     = custom_runName ?: workflow.runName
 summary['Reads']        = params.reads
@@ -1101,7 +1097,7 @@ process multiqc {
  */
 process output_documentation {
     tag "$prefix"
-    publishDir "${params.outdir}/Documentation", mode: 'copy'
+    publishDir "${params.outdir}/pipeline_info", mode: 'copy'
 
     input:
     file output_docs
@@ -1193,7 +1189,7 @@ workflow.onComplete {
     email_html = email_html.replaceAll(~/cid:ngilogo/, "data:image/png;base64,$ngilogo")
 
     // Write summary e-mail HTML to a file
-    def output_d = new File( "${params.outdir}/Documentation/" )
+    def output_d = new File( "${params.outdir}/pipeline_info/" )
     if( !output_d.exists() ) {
       output_d.mkdirs()
     }

diff --git a/nextflow.config b/nextflow.config
@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  nfcore/RNAseq Nextflow config file
  * -------------------------------------------------
@@ -118,7 +116,7 @@ dag {
 
 manifest {
   homePage = 'https://github.com/nf-core/RNAseq'
-  description = 'Nextflow RNA-Seq Best Practice analysis pipeline, part of the nf-core community.'
+  description = 'Nextflow RNA-Seq analysis pipeline, part of the nf-core community.'
   mainScript = 'main.nf'
 }
 

diff --git a/tests/install.sh b/tests/install.sh
@@ -6,6 +6,8 @@
 #     s = singularity
 #     t = nf-core/tools
 
+SGT_VER=2.4.5
+
 # Install Nextflow
 if [[ $1 = *n* ]]; then
   cd $HOME