Merge pull request #89 from drpatelh/master

Bump version to 1.0.0

Author: drpatelh

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/chipseq:dev
   # Fake the tag locally so that the pipeline runs properly
   # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/chipseq:dev nfcore/chipseq:dev
+  - docker tag nfcore/chipseq:dev nfcore/chipseq:1.0.0
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## v1.0.0 - [2019-06-05]
 Initial release of nf-core/chipseq.
 
 ### `Added`
@@ -14,6 +14,7 @@ Initial release of nf-core/chipseq.
 * Adapter trimming (Trim Galore!)
 * Map and filter reads (BWA, picard, SAMtools, BEDTools, BAMTools, Pysam)
 * Create library-size normalised bigWig tracks (BEDTools, bedGraphToBigWig)
+* Alignment QC metrics (Preseq, picard)
 * ChIP-seq QC metrics (deepTools, phantompeakqualtools)
 * Call and annotate broad/narrow peaks (MACS2, HOMER)
 * Create consensus set of peaks per antibody (BEDTools)

Dockerfile

@@ -4,4 +4,4 @@ LABEL authors="Philip Ewels" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-chipseq-1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-chipseq-1.0.0/bin:$PATH

assets/multiqc/multiqc_config.yaml

@@ -16,6 +16,7 @@ fn_clean_exts:
     - 'mLb'
     - '_peaks'
     - '_spp'
+    - '.spp'
 
 module_order:
     - fastqc:

conf/base.config

@@ -41,7 +41,6 @@ process {
   withName:get_software_versions {
     cache = false
   }
-
 }
 
 // Defaults config params, may be overwritten by later configs

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-chipseq-1.0dev
+name: nf-core-chipseq-1.0.0
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -559,7 +559,7 @@ process bwaMEM {
     }
     """
     bwa mem \\
-        -t $task.cpus\\
+        -t $task.cpus \\
         -M \\
         -R $rg \\
         ${index}/${bwa_base} \\
@@ -810,7 +810,7 @@ if (params.singleEnd){
 ///////////////////////////////////////////////////////////////////////////////
 
 /*
- * STEP 5.2 preseq analysis after merging libraries and before filtering
+ * STEP 5.1 preseq analysis after merging libraries and before filtering
  */
 process preseq {
     tag "$name"
@@ -834,7 +834,7 @@ process preseq {
 }
 
 /*
- * STEP 5.1 Picard CollectMultipleMetrics after merging libraries and filtering
+ * STEP 5.2 Picard CollectMultipleMetrics after merging libraries and filtering
  */
 process collectMultipleMetrics {
     tag "$name"

nextflow.config

@@ -86,7 +86,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/chipseq:dev'
+process.container = 'nfcore/chipseq:1.0.0'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -142,7 +142,7 @@ manifest {
   description = 'ChIP-seq peak-calling and differential analysis pipeline.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'
-  version = '1.0dev'
+  version = '1.0.0'
 }
 
 // Function to ensure that resource requirements don't go beyond