From 713d9cf07decbf8a063f065d788987d93567d75e Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 16 Jan 2019 16:52:11 +0100 Subject: [PATCH 1/2] small fixes --- Dockerfile | 4 ++-- buildReferences.nf | 24 ------------------------ containers/r-base/Dockerfile | 7 ++++--- 3 files changed, 6 insertions(+), 29 deletions(-) diff --git a/Dockerfile b/Dockerfile index 9b6674f9a5..bbadf8ff33 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,9 @@ FROM nfcore/base:latest LABEL \ - authors="Maxime.Garcia@scilifelab.se, Szilveszter.Juhos@scilifelab.se" \ + authors="maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se" \ description="Image with tools used in Sarek" \ - maintainer="Maxime Garcia , Szilveszter Juhos " + maintainer="Maxime Garcia , Szilveszter Juhos " COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a diff --git a/buildReferences.nf b/buildReferences.nf index 5d3f4d485e..6c4315b85e 100644 --- a/buildReferences.nf +++ b/buildReferences.nf @@ -212,30 +212,6 @@ def checkUppmaxProject() { return !(workflow.profile == 'slurm' && !params.project) } -def defReferencesFiles(genome) { - if (genome == "smallGRCh37") { - return [ - '1000G_phase1.indels.b37.small.vcf.gz', - '1000G_phase3_20130502_SNP_maf0.3.small.loci', - 'b37_cosmic_v74.noCHR.sort.4.1.small.vcf.gz', - 'dbsnp_138.b37.small.vcf.gz', - 'human_g1k_v37_decoy.small.fasta.gz', - 'Mills_and_1000G_gold_standard.indels.b37.small.vcf.gz', - 'small.intervals' - ] - } else if (genome == "GRCh37") { - return [ - '1000G_phase1.indels.b37.vcf.gz', - '1000G_phase3_20130502_SNP_maf0.3.loci.tar.bz2', - 'GRCh37_Cosmic_v83.vcf.tar.bz2', - 'dbsnp_138.b37.vcf.gz', - 'human_g1k_v37_decoy.fasta.gz', - 'Mills_and_1000G_gold_standard.indels.b37.vcf.gz', - 'wgs_calling_regions.grch37.list' - ] - } else exit 1, "Can't build this reference genome" -} - def grabRevision() { // Return the same string executed from github or not return workflow.revision ?: workflow.commitId ?: workflow.scriptId.substring(0,10) diff --git a/containers/r-base/Dockerfile b/containers/r-base/Dockerfile index 2f38953fa6..5f43f3a43f 100644 --- a/containers/r-base/Dockerfile +++ b/containers/r-base/Dockerfile @@ -1,8 +1,9 @@ FROM r-base:3.3.2 -LABEL author="Maxime Garcia" \ -description="R 3.3.2 image for use in Sarek" \ -maintainer="maxime.garcia@scilifelab.se" +LABEL \ + author="Maxime Garcia" \ + description="R 3.3.2 image for use in Sarek" \ + maintainer="maxime.garcia@scilifelab.se" # Install libraries RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile \ From a49bba9026588a083db92c3b73ed0ab5792ec0d8 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 17 Jan 2019 16:37:54 +0100 Subject: [PATCH 2/2] update CHANGELOG [skip ci] --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aaf352769f..ecf373369c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#710](https://github.com/SciLifeLab/Sarek/pull/710) - Improve release checklist and script - [#711](https://github.com/SciLifeLab/Sarek/pull/711) - Improve configuration priorities +### `Removed` +- [#715](https://github.com/SciLifeLab/Sarek/pull/715) - Remove `defReferencesFiles` function from `buildReferences.nf` + ## [2.2.2] - 2018-12-19 ### `Added`