Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Install Ascat with bioconda #32

Merged
merged 4 commits into from
Sep 5, 2019
Merged

Install Ascat with bioconda #32

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
0d67dde
install ASCAT in the main container
maxulysse Sep 4, 2019
dde1dab
fix linting for MD
maxulysse Sep 4, 2019
298083a
clean up environment.yml
maxulysse Sep 5, 2019
4ae1623
Merge remote-tracking branch 'upstream/dev' into ascat
maxulysse Sep 5, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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`

Expand All @@ -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`

Expand Down
92 changes: 31 additions & 61 deletions docs/containers.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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
Expand All @@ -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
4 changes: 1 addition & 3 deletions environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down