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

Jump to bottom

More polishing before 2.6 release #158

Merged
merged 8 commits into from
Mar 17, 2020
Merged

More polishing before 2.6 release #158

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
4d2f1c8
fix typo
maxulysse Mar 13, 2020
2c595e5
Merge remote-tracking branch 'upstream/dev' into snpEff
maxulysse Mar 13, 2020
212a7b3
add ggplot2
maxulysse Mar 17, 2020
f2f83ad
update ggplot2 version
maxulysse Mar 17, 2020
1900b1e
update docs
maxulysse Mar 17, 2020
8b6177d
Merge branch 'dev' into snpEff
maxulysse Mar 17, 2020
b2cf4b7
update CHANGELOG
maxulysse Mar 17, 2020
1f9914d
Merge branch 'snpEff' of github.com:MaxUlysse/nf-core_sarek into snpEff
maxulysse Mar 17, 2020
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
4 changes: 3 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
- [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
- [#141](https://github.com/nf-core/sarek/pull/141) - Add containers for `WBcel235`
- [#150](https://github.com/nf-core/sarek/pull/150), [#151](https://github.com/nf-core/sarek/pull/151), [#154](https://github.com/nf-core/sarek/pull/154) - Add AWS mega test GitHub Actions
- [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` v `3.3.0`

### `Changed`

Expand All @@ -40,7 +41,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38`
- [#152](https://github.com/nf-core/sarek/pull/152) - Update docs
- [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158) - Update docs

### `Fixed`

Expand All @@ -60,6 +61,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
- [#146](https://github.com/nf-core/sarek/pull/146) - Fix `--no_intervals` for `Mutect2` cf [#135](https://github.com/nf-core/sarek/issues/135)
- [#156](https://github.com/nf-core/sarek/pull/156) - Fix typos
- [#156](https://github.com/nf-core/sarek/pull/156) - Fix issues with `dbsnp` files while using only `Sention` tools
- [#158](https://github.com/nf-core/sarek/pull/158) - Fix typo with `params.snpeff_cache` to decide containers for `snpEff`

### `Deprecated`

Expand Down
2 changes: 1 addition & 1 deletion conf/base.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ process {
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
}
withName:Snpeff {
container = {(params.annotation_cache && params.snpEff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"}
container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"}
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
}
withLabel:VEP {
Expand Down
5 changes: 3 additions & 2 deletions docs/containers.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ For annotation, the main container can be used, but the cache has to be download
- Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.3.2
- Contain **[GATK4-spark](https://github.com/broadinstitute/gatk)** 4.1.4.1
- Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0
- Contain **[ggplot2](https://github.com/tidyverse/ggplot2)** 3.3.0
- Contain **[HTSlib](https://github.com/samtools/htslib)** 1.9
- Contain **[Manta](https://github.com/Illumina/manta)** 1.6.0
- Contain **[MultiQC](https://github.com/ewels/MultiQC/)** 1.8
Expand All @@ -41,14 +42,14 @@ For annotation, the main container can be used, but the cache has to be download

- Based on `nfcore/base:1.9`
- Contain **[snpEff](http://snpeff.sourceforge.net/)** 4.3.1t
- Contains cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1`
- Contains cache for `GRCh37`, `GRCh38`, `GRCm38`, `CanFam3.1` or `WBcel235`

### sarekvep [![sarekvep-docker status](https://img.shields.io/docker/automated/nfcore/sarekvep.svg)](https://hub.docker.com/r/nfcore/sarekvep)

- Based on `nfcore/base:1.9`
- Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0
- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 99.2
- Contain cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1`
- Contain cache for `GRCh37`, `GRCh38`, `GRCm38`, `CanFam3.1` or `WBcel235`

## Building your own

Expand Down
3 changes: 2 additions & 1 deletion environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,4 +30,5 @@ dependencies:
- bioconda::trim-galore=0.6.5
- bioconda::vcfanno=0.3.2
- bioconda::vcftools=0.1.16
- conda-forge::pigz=2.3.4
- conda-forge::pigz=2.3.4
- conda-forge::r-ggplot2=3.3.0