diff --git a/.travis.yml b/.travis.yml index b641d3f0..f86c8abf 100644 --- a/.travis.yml +++ b/.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: diff --git a/CHANGELOG.md b/CHANGELOG.md index 34bbe545..6c2fbe56 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/Dockerfile b/Dockerfile index bdde32f4..c43fecf6 100644 --- a/Dockerfile +++ b/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 diff --git a/README.md b/README.md index c80f40b1..543f009f 100644 --- a/README.md +++ b/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/) diff --git a/conf/base.config b/conf/base.config index 12f1cff4..722a01ad 100644 --- a/conf/base.config +++ b/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/' -} diff --git a/main.nf b/main.nf index 62d81b79..51b84f3e 100755 --- a/main.nf +++ b/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)}: $v" }.join("\n") log.info "-\033[2m--------------------------------------------------\033[0m-" diff --git a/nextflow.config b/nextflow.config index 9d285a6a..c758ab92 100644 --- a/nextflow.config +++ b/nextflow.config @@ -69,7 +69,7 @@ params { // Options: Other help = false outdir = './results' - igenomes_base = "./iGenomes" + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false max_multiqc_email_size = 25.MB tracedir = "${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' }