From 747f8cdb7c0be1b9c9fedc4e54ffe96440c46cb5 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 5 Sep 2019 14:08:19 +0200 Subject: [PATCH] Install Ascat with bioconda (#32) * install ASCAT in the main container * update docs * clean up environment.yml --- CHANGELOG.md | 2 + docs/containers.md | 92 ++++++++++++++++------------------------------ environment.yml | 4 +- 3 files changed, 34 insertions(+), 64 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 137b11519a..f0b9106c89 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -73,6 +73,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) - [#18](https://github.com/nf-core/sarek/pull/18), [#21](https://github.com/nf-core/sarek/pull/21) - Update logo - [#21](https://github.com/nf-core/sarek/pull/21) - Moved smallGRCh37 path to `genomes.config` - [#31](https://github.com/nf-core/sarek/pull/31) - Move extra CI to GitHub Actions nf-core extra CI +- [#32](https://github.com/nf-core/sarek/pull/32) - Install `ASCAT` with `conda` in the `environment.yml` file ### `Removed` @@ -81,6 +82,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) - [#13](https://github.com/nf-core/sarek/pull/13) - Removed `CompressVCF` - [#18](https://github.com/nf-core/sarek/pull/18) - Removed params `--noReports` - [#31](https://github.com/nf-core/sarek/pull/31) - Remove extra CI from Travis CI and GitHub Actions nf-core CI +- [#32](https://github.com/nf-core/sarek/pull/32) - Clean up `environment.yml` file ### `Fixed` diff --git a/docs/containers.md b/docs/containers.md index 20d7ee30e0..9f31f477a0 100644 --- a/docs/containers.md +++ b/docs/containers.md @@ -11,44 +11,43 @@ For annotation, the main container can be used, but the cache has to be download ## What is actually inside the containers -### sarek [![sarek-docker status][sarek-docker-badge]][sarek-docker-link] +### sarek [![sarek-docker status](https://img.shields.io/docker/automated/nfcore/sarek.svg)](https://hub.docker.com/r/nfcore/sarek) - Based on `nfcore/base:latest` -- Contain **[AlleleCount][allelecount-link]** 4.0.2 -- Contain **[BCFTools][bcftools-link]** 1.9 -- Contain **[BWA][bwa-link]** 0.7.17 -- Contain **[FastQC][fastqc-link]** 0.11.8 -- Contain **[FreeBayes][freebayes-link]** 1.2.0 -- Contain **[GATK4][gatk4-link]** 4.1.2.0 -- Contain **[GeneSplicer][genesplicer-link]** 1.0 -- Contain **[HTSlib][htslib-link]** 1.9 -- Contain **[IGVtools][igvtools-link]** 2.3.93 -- Contain **[Manta][manta-link]** 1.5.0 -- Contain **[MultiQC][multiqc-link]** 1.7 -- Contain **[Qualimap][qualimap-link]** 2.2.2b -- Contain **[R][r-link]** 3.5.1 -- Contain **[RColorBrewer][rcolorbrewer-link]** 1.1 -- Contain **[Rtracklayer][rtracklayer-link]** 1.42.1 -- Contain **[samtools][samtools-link]** 1.9 -- Contain **[snpEff][snpeff-link]** 4.3.1t -- Contain **[Strelka2][strelka-link]** 2.9.10 -- Contain **[TIDDIT][tiddit-link]** 2.7.1 -- Contain **[VCFanno][vcfanno-link]** 0.3.1 -- Contain **[VCFtools][vcftools-link]** 0.1.16 -- Contain **[VEP][vep-link]** 96.0 - -### sareksnpeff [![sareksnpeff-docker status][sareksnpeff-docker-badge]][sareksnpeff-docker-link] +- Contain **[ASCAT](https://github.com/Crick-CancerGenomics/ascat)** 2.5.2 +- Contain **[AlleleCount](https://github.com/cancerit/alleleCount)** 4.0.2 +- Contain **[BCFTools](https://github.com/samtools/bcftools)** 1.9 +- Contain **[BWA](https://github.com/lh3/bwa)** 0.7.17 +- Contain **[Control-FREEC](https://github.com/BoevaLab/FREEC)** 11.4 +- Contain **[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)** 0.11.8 +- Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.2.0 +- Contain **[GATK4](https://github.com/broadinstitute/gatk)** 4.1.2.0 +- Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0 +- Contain **[HTSlib](https://github.com/samtools/htslib)** 1.9 +- Contain **[IGVtools](http://software.broadinstitute.org/software/igv/)** 2.3.93 +- Contain **[Manta](https://github.com/Illumina/manta)** 1.5.0 +- Contain **[MultiQC](https://github.com/ewels/MultiQC/)** 1.7 +- Contain **[Qualimap](http://qualimap.bioinfo.cipf.es)** 2.2.2b +- Contain **[samtools](https://github.com/samtools/samtools)** 1.9 +- Contain **[snpEff](http://snpeff.sourceforge.net/)** 4.3.1t +- Contain **[Strelka2](https://github.com/Illumina/strelka)** 2.9.10 +- Contain **[TIDDIT](https://github.com/SciLifeLab/TIDDIT)** 2.7.1 +- Contain **[VCFanno](https://github.com/brentp/vcfanno)** 0.3.1 +- Contain **[VCFtools](https://vcftools.github.io/index.html)** 0.1.16 +- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 95.2 + +### sareksnpeff [![sareksnpeff-docker status](https://img.shields.io/docker/automated/nfcore/sareksnpeff.svg)](https://hub.docker.com/r/nfcore/sareksnpeff) - Based on `nfcore/base:latest` -- Contain **[snpEff][snpeff-link]** 4.3.1t -- Contain cache for `GRCh37`, `GRCh38`, or `GRCm38` +- Contain **[snpEff](http://snpeff.sourceforge.net/)** 4.3.1t +- Contain cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1` -### sarekvep [![sarekvep-docker status][sarekvep-docker-badge]][sarekvep-docker-link] +### sarekvep [![sarekvep-docker status](https://img.shields.io/docker/automated/nfcore/sarekvep.svg)](https://hub.docker.com/r/nfcore/sarekvep) - Based on `nfcore/base:latest` -- Contain **[GeneSplicer][genesplicer-link]** 1.0 -- Contain **[VEP][vep-link]** 96.0 -- Contain cache for `GRCh37`, `GRCh38`, or `GRCm38` +- Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0 +- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 95.2 +- Contain cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1` ## Using helper script @@ -72,7 +71,7 @@ Default:`dev` ### Genome: -g -Specify which release genome to use for annotation containers (`sareksnpeff`, `sarekvep`): `GRCh37`, `GRCh38`, `smallGRCh37`, `CanFan3.1`, `GRCm38`. +Specify which release genome to use for annotation containers (`sareksnpeff`, `sarekvep`): `smallGRCh37`, `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1`. Default:`smallGRCh37` ### Singularity @@ -89,32 +88,3 @@ That will build the main container, plus the annotation containers (`sareksnpeff Our containers are designed using [Conda](https://conda.io/). The `environment.yml` file can easilly be modified if particular versions of tools are more suited to your needs. - -[allelecount-link]: https://github.com/cancerit/alleleCount -[bcftools-link]: https://github.com/samtools/bcftools -[bwa-link]: https://github.com/lh3/bwa -[fastqc-link]: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ -[freebayes-link]: https://github.com/ekg/freebayes -[gatk4-link]: https://github.com/broadinstitute/gatk -[genesplicer-link]: https://ccb.jhu.edu/software/genesplicer/ -[htslib-link]: https://github.com/samtools/htslib -[igvtools-link]: http://software.broadinstitute.org/software/igv/ -[manta-link]: https://github.com/Illumina/manta -[multiqc-link]: https://github.com/ewels/MultiQC/ -[qualimap-link]: http://qualimap.bioinfo.cipf.es -[r-link]: https://www.r-project.org/ -[rcolorbrewer-link]: https://CRAN.R-project.org/package=RColorBrewer -[rtracklayer-link]: https://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html -[samtools-link]: https://github.com/samtools/samtools -[sarek-docker-badge]: https://img.shields.io/docker/automated/nfcore/sarek.svg -[sarek-docker-link]: https://hub.docker.com/r/nfcore/sarek -[snpeff-link]: http://snpeff.sourceforge.net/ -[sareksnpeff-docker-badge]: https://img.shields.io/docker/automated/nfcore/sareksnpeff.svg -[sareksnpeff-docker-link]: https://hub.docker.com/r/nfcore/sareksnpeff -[strelka-link]: https://github.com/Illumina/strelka -[tiddit-link]: https://github.com/SciLifeLab/TIDDIT -[vcfanno-link]: https://github.com/brentp/vcfanno -[vcftools-link]: https://vcftools.github.io/index.html -[vep-link]: https://github.com/Ensembl/ensembl-vep -[sarekvep-docker-badge]: https://img.shields.io/docker/automated/nfcore/sarekvep.svg -[sarekvep-docker-link]: https://hub.docker.com/r/nfcore/sarekvep diff --git a/environment.yml b/environment.yml index 968f8d3d8f..761004c21c 100644 --- a/environment.yml +++ b/environment.yml @@ -6,10 +6,8 @@ channels: - bioconda - defaults dependencies: - - r-rcolorbrewer=1.1_2 - - r-base=3.5.1 + - ascat=2.5.2 - bcftools=1.9 - - bioconductor-rtracklayer=1.42.1 - bwa=0.7.17 - cancerit-allelecount=4.0.2 - control-freec=11.4