Merge pull request #115 from drpatelh/master

Address comments for PR #114 (Dev > Master)

Author: drpatelh

.travis.yml

@@ -30,7 +30,7 @@ install:
   - sudo apt-get install npm && npm install -g markdownlint-cli
 
 env:
-  - NXF_VER='19.04.0' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='19.10.0' # Specify a minimum NF version that should be tested and work
   - NXF_VER='' # Plus: get the latest NF version and check that it works
 
 script:

CHANGELOG.md

@@ -5,33 +5,54 @@ 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).
 
-## [1.1.0] - 2019-11-01
+## [1.1.0] - 2019-11-05
 
 ### `Added`
 
 * [#46](https://github.com/nf-core/atacseq/issues/46) - Missing gene_bed path in igenomes config
-* Capitalised process names
-* Add quick start information to main README
 * Update template to tools `1.7`
 * Add `--trim_nextseq` parameter
-* Added `CITATIONS.md` file
+* Add `CITATIONS.md` file
+* Capitalised process names
 
 ### `Fixed`
 
+* **Change all parameters from `camelCase` to `snake_case` (see [Deprecated](#Deprecated))**
 * [#44](https://github.com/nf-core/atacseq/issues/44) - Output directory missing: macs2/consensus/deseq2
 * [#45](https://github.com/nf-core/atacseq/issues/45) - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
 * [#46](https://github.com/nf-core/atacseq/issues/46) - Stage blacklist file in channel properly
 * [#50](https://github.com/nf-core/atacseq/issues/50) - HOMER number of peaks does not correspond to found MACS2 peaks
+* Fixed bug in UpSetR peak intersection plot
 * Increase default resource requirements in `base.config`
 * Increase process-specific requirements based on user-reported failures
-* Change parameter `saveGenomeIndex` to `save_reference`
-* Change parameter `--design` to `--input`
-* Change all parameters from `camelCase` to `snake_case`
-* Fixed bug in UpSetR peak intersection plot
 
 ### `Dependencies`
 
-* Bump Nextflow version to `19.04.0`
+* Update Nextflow `0.32.0` -> `19.10.0`
+
+### `Deprecated`
+
+| Deprecated                   | Replacement               |
+|------------------------------|---------------------------|
+| `--design`                   | `--input`                 |
+| `--singleEnd`                | `--single_end`            |
+| `--saveGenomeIndex`          | `--save_reference`        |
+| `--skipTrimming`             | `--skip_trimming`         |
+| `--saveTrimmed`              | `--save_trimmed`          |
+| `--keepDups`                 | `--keep_dups`             |
+| `--keepMultiMap`             | `--keep_multi_map`        |
+| `--saveAlignedIntermediates` | `--save_align_intermeds`  |
+| `--narrowPeak`               | `--narrow_peak`           |
+| `--saveMACSPileup`           | `--save_macs_pileup`      |
+| `--skipDiffAnalysis`         | `--skip_diff_analysis`    |
+| `--skipFastQC`               | `--skip_fastqc`           |
+| `--skipPicardMetrics`        | `--skip_picard_metrics`   |
+| `--skipPreseq`               | `--skip_preseq`           |
+| `--skipPlotProfile`          | `--skip_plot_profile`     |
+| `--skipPlotFingerprint`      | `--skip_plot_fingerprint` |
+| `--skipSpp`                  | `--skip_spp`              |
+| `--skipIGV`                  | `--skip_igv`              |
+| `--skipMultiQC`              | `--skip_multiqc`          |
 
 ## [1.0.0] - 2019-06-06
 

Dockerfile

@@ -2,7 +2,12 @@ FROM nfcore/base:1.7
 LABEL authors="Philip Ewels" \
       description="Docker image containing all requirements for nf-core/chipseq pipeline"
 
+# Install the conda environment
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-RUN conda env export --name nf-core-chipseq-1.1.0 > nf-core-chipseq-1.1.0.yml
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
 ENV PATH /opt/conda/envs/nf-core-chipseq-1.1.0/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-chipseq-1.1.0 > nf-core-chipseq-1.1.0.yml

README.md

@@ -1,7 +1,7 @@
 # ![nf-core/chipseq](docs/images/nf-core-chipseq_logo.png)
 
 [![Build Status](https://travis-ci.com/nf-core/chipseq.svg?branch=master)](https://travis-ci.com/nf-core/chipseq)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.04.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/chipseq.svg)](https://hub.docker.com/r/nfcore/chipseq/)

conf/base.config

@@ -43,11 +43,3 @@ process {
   }
 
 }
-
-params {
-  // Defaults only, expecting to be overwritten
-  max_memory = 128.GB
-  max_cpus = 16
-  max_time = 240.h
-  igenomes_base = 's3://ngi-igenomes/igenomes/'
-}

main.nf

@@ -256,17 +256,17 @@ summary['Working Dir']            = workflow.workDir
 summary['Script Dir']             = workflow.projectDir
 summary['User']                   = workflow.userName
 if (workflow.profile == 'awsbatch') {
-   summary['AWS Region']          = params.awsregion
-   summary['AWS Queue']           = params.awsqueue
+    summary['AWS Region']         = params.awsregion
+    summary['AWS Queue']          = params.awsqueue
 }
 summary['Config Profile']         = workflow.profile
 if (params.config_profile_description) summary['Config Description'] = params.config_profile_description
 if (params.config_profile_contact)     summary['Config Contact']     = params.config_profile_contact
 if (params.config_profile_url)         summary['Config URL']         = params.config_profile_url
 if (params.email || params.email_on_fail) {
-  summary['E-mail Address']       = params.email
-  summary['E-mail on failure']    = params.email_on_fail
-  summary['MultiQC Max Size']     = params.max_multiqc_email_size
+    summary['E-mail Address']     = params.email
+    summary['E-mail on failure']  = params.email_on_fail
+    summary['MultiQC Max Size']   = params.max_multiqc_email_size
 }
 log.info summary.collect { k,v -> "${k.padRight(20)}: $v" }.join("\n")
 log.info "-\033[2m--------------------------------------------------\033[0m-"

nextflow.config

@@ -69,7 +69,7 @@ params {
   // Options: Other
   help = false
   outdir = './results'
-  igenomes_base = "./iGenomes"
+  igenomes_base = 's3://ngi-igenomes/igenomes/'
   igenomes_ignore = false
   max_multiqc_email_size = 25.MB
   tracedir = "${params.outdir}/pipeline_info"
@@ -81,6 +81,11 @@ params {
   hostnames = false
   clusterOptions = false
 
+  // Defaults only, expecting to be overwritten
+  max_memory = 128.GB
+  max_cpus = 16
+  max_time = 240.h
+
 }
 
 // Container slug. Stable releases should specify release tag!
@@ -120,6 +125,11 @@ if (!params.igenomes_ignore) {
 // Increase time available to build conda environment
 conda { createTimeout = "60 min" }
 
+// Export this variable to prevent local Python libraries from conflicting with those in the container
+env {
+  PYTHONNOUSERSITE = 1
+}
+
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
@@ -146,7 +156,7 @@ manifest {
   homePage = 'https://github.com/nf-core/chipseq'
   description = 'ChIP-seq peak-calling and differential analysis pipeline.'
   mainScript = 'main.nf'
-  nextflowVersion = '>=19.04.0'
+  nextflowVersion = '>=19.10.0'
   version = '1.1.0'
 }