From edf3b7ec1060f0d3a4140739b2babaa23fea4696 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 13:33:47 +0000 Subject: [PATCH 01/16] Move params section to nextflow.config --- conf/base.config | 8 -------- 1 file changed, 8 deletions(-) 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/' -} From 8f99518de27c38b0cd5851f53ef7150dde8b61b9 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 13:33:52 +0000 Subject: [PATCH 02/16] Move params section to nextflow.config --- nextflow.config | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 9d285a6a..ab4f2950 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! From d8901d06fdd1507a2191749ace2c158c38e41186 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:09:26 +0000 Subject: [PATCH 03/16] Update CHANGELOG --- CHANGELOG.md | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 34bbe545..0a88f38f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,29 +10,48 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `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 +* Capitalised process names ### `Fixed` +* **Change all parameters from `camelCase` to `snake_case`** * [#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 * 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` +### `Deprecated` + +* `--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 Initial release of nf-core/chipseq pipeline. From 2f5755f23abc0e79d91a2cb8a7a3c0042c6d896e Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:13:46 +0000 Subject: [PATCH 04/16] Update CHANGELOG --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a88f38f..566146bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,12 +12,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * [#46](https://github.com/nf-core/atacseq/issues/46) - Missing gene_bed path in igenomes config * 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`** +* **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 From d8d8c5067d5d53518a87200659643742fd9d9e09 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:20:49 +0000 Subject: [PATCH 05/16] Add parameters in table --- CHANGELOG.md | 47 +++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 45 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 566146bc..be71fb59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,14 +17,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` -* **Change all parameters from `camelCase` to `snake_case` (see [Deprecated](#Deprecated)** +* **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 -* Fixed bug in UpSetR peak intersection plot ### `Dependencies` @@ -32,6 +32,49 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Deprecated` +| Deprecated | Added | +|------------------------------|---------------------------| +| `--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` | + +* `--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` + + * `--design` -> `--input` * `--singleEnd` -> `--single_end` * `--saveGenomeIndex` -> `--save_reference` From 030b4dd53f05a64221ac08bb004a6bb273988763 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:22:46 +0000 Subject: [PATCH 06/16] Add params table --- CHANGELOG.md | 43 +------------------------------------------ 1 file changed, 1 insertion(+), 42 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index be71fb59..d692be6d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,7 +32,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Deprecated` -| Deprecated | Added | +| Deprecated | Replacement | |------------------------------|---------------------------| | `--design` | `--input` | | `--singleEnd` | `--single_end` | @@ -54,47 +54,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. | `--skipIGV` | `--skip_igv` | | `--skipMultiQC` | `--skip_multiqc` | -* `--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` - - -* `--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 Initial release of nf-core/chipseq pipeline. From ec4d2cc54e01d69452df3e91769220dac64a1d3a Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:26:58 +0000 Subject: [PATCH 07/16] Fix spacing --- main.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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-" From bc8473d57c18201ffe21eabe8daba2bf651e2c2d Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:27:15 +0000 Subject: [PATCH 08/16] Change date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d692be6d..1e9bdf12 100644 --- a/CHANGELOG.md +++ b/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). -## [1.1.0] - 2019-11-01 +## [1.1.0] - 2019-11-04 ### `Added` From 43118e7774b28e5dea625375410cb9cd328ebdb0 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:36:04 +0000 Subject: [PATCH 09/16] Update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1e9bdf12..8ac3b6a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,7 +28,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Dependencies` -* Bump Nextflow version to `19.04.0` +* Update `Nextflow 0.32.0` -> `19.04.0` ### `Deprecated` From f95ce93c174648d92e320e54719bcd8a836dc652 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 14:37:35 +0000 Subject: [PATCH 10/16] Update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ac3b6a9..e8f89c0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,7 +28,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Dependencies` -* Update `Nextflow 0.32.0` -> `19.04.0` +* Update Nextflow `0.32.0` -> `19.04.0` ### `Deprecated` From 51311bcf49fd9e285506e778361a01f912e4559a Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 16:53:20 +0000 Subject: [PATCH 11/16] Export PYTHONNOUSERSITE in Dockerfile --- Dockerfile | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index bdde32f4..8af03174 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,15 @@ 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 + +# Prevent Python from loading packages from outside the container +ENV PYTHONNOUSERSITE=1 From e9413a062a57d98741c4828695974d9dcf684473 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 18:00:53 +0000 Subject: [PATCH 12/16] Add PYTHONNOUSERSITE to nextflow.config --- nextflow.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nextflow.config b/nextflow.config index ab4f2950..36196977 100644 --- a/nextflow.config +++ b/nextflow.config @@ -125,6 +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'] From 977e4b6a19cbd1a7648ff7015791a017b5dbefa3 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 18:11:07 +0000 Subject: [PATCH 13/16] Bump Nextflow to 19.10.0 --- .travis.yml | 2 +- README.md | 2 +- nextflow.config | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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/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/nextflow.config b/nextflow.config index 36196977..c758ab92 100644 --- a/nextflow.config +++ b/nextflow.config @@ -156,7 +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' } From b9beb149a6805f3682c85a857cb0f5c6fd59728d Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 18:15:14 +0000 Subject: [PATCH 14/16] Update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e8f89c0f..768d00a0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,7 +28,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Dependencies` -* Update Nextflow `0.32.0` -> `19.04.0` +* Update Nextflow `0.32.0` -> `19.10.0` ### `Deprecated` From 26396bcb9fa246ce462cf7710fb14ab96427e638 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 1 Nov 2019 18:30:36 +0000 Subject: [PATCH 15/16] Remove PYTHONNOUSERSITE from Dockerfile --- Dockerfile | 3 --- 1 file changed, 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8af03174..c43fecf6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,6 +11,3 @@ 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 - -# Prevent Python from loading packages from outside the container -ENV PYTHONNOUSERSITE=1 From 7456784d2c25518cf79665f85b74a0a5e7a50f06 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 4 Nov 2019 11:22:36 +0000 Subject: [PATCH 16/16] Update CHANGELOG date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 768d00a0..6c2fbe56 100644 --- a/CHANGELOG.md +++ b/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). -## [1.1.0] - 2019-11-04 +## [1.1.0] - 2019-11-05 ### `Added`