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Merge pull request #89 from drpatelh/master
Bump version to 1.0.0
2 parents 83dc9cb + 823cdec commit 44a346a

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.travis.yml

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

CHANGELOG.md

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

Dockerfile

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

assets/multiqc/multiqc_config.yaml

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

conf/base.config

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withName:get_software_versions {
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cache = false
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}
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}
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// Defaults config params, may be overwritten by later configs

environment.yml

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

main.nf

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}
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"""
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bwa mem \\
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-t $task.cpus\\
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-t $task.cpus \\
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-M \\
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-R $rg \\
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${index}/${bwa_base} \\
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///////////////////////////////////////////////////////////////////////////////
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/*
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* STEP 5.2 preseq analysis after merging libraries and before filtering
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* STEP 5.1 preseq analysis after merging libraries and before filtering
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*/
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process preseq {
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tag "$name"
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}
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/*
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* STEP 5.1 Picard CollectMultipleMetrics after merging libraries and filtering
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* STEP 5.2 Picard CollectMultipleMetrics after merging libraries and filtering
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*/
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process collectMultipleMetrics {
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tag "$name"

nextflow.config

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

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