Update docs

CHANGELOG.md

@@ -17,13 +17,17 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `vepCacheVersion` is now defined in `conf/genomes.config` or `conf/igenomes.config`
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `snpeff` and `vep` containers are now built with conda
 -   [#716](https://github.com/SciLifeLab/Sarek/pull/716) - Update paths to containers and iGenomes
+-   [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Update `Sarek-data` submodule
+-   [#723](https://github.com/SciLifeLab/Sarek/pull/723), [#725](https://github.com/SciLifeLab/Sarek/pull/725) - Update docs
 -   [#724](https://github.com/SciLifeLab/Sarek/pull/724) - Improved AwsBatch configuration
 
 ### `Added`
+-   [#628](https://github.com/SciLifeLab/Sarek/pull/628), [#722](https://github.com/SciLifeLab/Sarek/pull/722) - `ASCAT` now use `.gc` file
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - Possibility to use cache wen annotating with `snpEff` and `VEP`
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - New `--annotation_cache`, `--snpEff_cache`, `--vep_cache` parameters
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - Helper script to download `snpeff` and `VEP` cache files
 -   [#719](https://github.com/SciLifeLab/Sarek/pull/719) - Annotation documentation
+-   [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Add path to ASCAT `.gc` file in `igenomes.config`
 
 ### `Removed`
 -   [#715](https://github.com/SciLifeLab/Sarek/pull/715) - Remove `defReferencesFiles` function from `buildReferences.nf`
@@ -44,8 +48,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#694](https://github.com/SciLifeLab/Sarek/pull/694) - Add monochrome and grey logos for light or dark background
 -   [#698](https://github.com/SciLifeLab/Sarek/pull/698) - Add btb profile for munin server
 -   [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Add font-ttf-dejavu-sans-mono `2.37` and fontconfig `2.12.6` to container
--   [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Update `Sarek-data` submodule
--   [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Add path to ASCAT `.gc` file in `igenomes.config`
 
 ### `Changed`
 

docs/CONTAINERS.md

@@ -1,71 +1,19 @@
 # Containers
 
-Subsets of all containers can be downloaded:
+Our main container is designed using Bioconda to install most of the tools used in Sarek:
+- [sarek](#sarek-)
 
-- For processing, germline variant calling and Reports:
-  - [sarek](#sarek-)
-- For somatic variant calling, add:
-  - [r-base](#r-base-)
-  - [runallelecount](#runallelecount-)
-- For annotation for GRCh37, you will need:
+For annotation, the main container can be used, but the cache has to be downloaded, or additional containers are available with cache (see [annotation guide](ANNOTATION.md)):
+- For GRCh37:
   - [snpeffgrch37](#snpeffgrch37-)
   - [vepgrch37](#vepgrch37-)
-- For annotation for GRCh38, you will need:
+- For GRCh38:
   - [snpeffgrch38](#snpeffgrch38-)
   - [vepgrch38](#vepgrch38-)
-- For annotation with cache use:
-  - [sarek](#sarek-)
-
-## Building
-
-Use the Nextflow script to build and/or push containers from Docker and/or Singularity.
-
-All the containers have built in UPPMAX directories, so there is no need to add them for use on UPPMAX clusters.
-- See the [Singularity UPPMAX guide](https://www.uppmax.uu.se/support-sv/user-guides/singularity-user-guide/)
-
-### Usage
-
-```bash
-nextflow run buildContainers.nf [--docker] [--singularity] /
-[--containerPath <path>] [--push] [--containers <container1[,container2..]>] /
-[--repository <repository>] [--tag tag]
-```
-
-- `--containers`: Choose which containers to build.
-Default: `all`.
-Possible values (to separate by commas):
-  - `all` -  all available containers.
-  - `r-base` - the [r-base](#r-base-) container.
-  - `runallelecount` - the [runallelecount](#runallelecount-) container.
-  - `sarek` - the [sarek](#sarek-) container.
-  - `snpeffgrch37` - the [snpeffgrch37](#snpeffgrch37-) container.
-  - `snpeffgrch38` - the [snpeffgrch38](#snpeffgrch38-) container.
-  - `vepgrch37` - the [vepgrch37](#vepgrch37-) container.
-  - `vepgrch38` - the [vepgrch38](#vepgrch38-) container.
-
-- `--docker`: Build containers using `Docker`
-- `--push`: Push containers to `DockerHub`
-- `--repository`: Build containers under given repository.
-Default: `maxulysse`
-- `--singularity`: Build containers using `Singularity`.
-- `--containerPath`: Select where to download containers.
-Default: `$PWD`
-- `--tag`: Build containers using given tag.
-Default is version number.
-
-### Example
 
-```bash
-nextflow run buildContainers.nf --docker --singularity --push --containers sarek
-```
-
-### For lazy users
-We provide script to build/push or pull all containers
-```bash
-./scripts/do_all.sh        # Build all docker containers
-./scripts/do_all.sh --push # Build and push all Docker containers into DockerHub
-./scripts/do_all.sh --pull # Pull all containers from DockerHub with Singularity
-```
+Additional containers need to be downloaded for somatic variant calling with ASCAT:
+  - [r-base](#r-base-)
+  - [runallelecount](#runallelecount-)
 
 ## What is actually inside the containers
 
@@ -103,25 +51,79 @@ We provide script to build/push or pull all containers
 
 - Based on `nfcore/base:latest`
 - Contain **[snpEff][snpeff-link]** 4.3.1t
-- Contain GRCh37.75
+- Contain cache for GRCh37.75
 
 ### snpeffgrch38 [![snpeffgrch38-docker status][snpeffgrch38-docker-badge]][snpeffgrch38-docker-link]
 
 - Based on `nfcore/base:latest`
 - Contain **[snpEff][snpeff-link]** 4.3.1t
-- Contain GRCh38.86
+- Contain cache for GRCh38.86
 
 ### vepgrch37 [![vepgrch37-docker status][vepgrch37-docker-badge]][vepgrch37-docker-link]
 
 - Based on `nfcore/base:latest`
 - Contain **[VEP][vep-link]** 95.1
-- Contain GRCh37
+- Contain cache for GRCh37 version 95
 
 ### vepgrch38 [![vepgrch38-docker status][vepgrch38-docker-badge]][vepgrch38-docker-link]
 
 - Based on `nfcore/base:latest`
 - Contain **[VEP][vep-link]** 95.1
-- Contain GRCh38
+- Contain cache for GRCh38 version 95
+
+## Building
+
+A Nextflow script is provided to build and/or push containers from Docker, or build for Singularity.
+
+### Usage
+
+```bash
+nextflow run buildContainers.nf [--docker] [--singularity] /
+[--containerPath <path>] [--push] [--containers <container1[,container2..]>] /
+[--repository <repository>] [--tag tag]
+```
+
+- `--containers`: Choose which containers to build.
+Default: `all`.
+Possible values (to separate by commas):
+  - `all` -  all available containers.
+  - `r-base` - the [r-base](#r-base-) container.
+  - `runallelecount` - the [runallelecount](#runallelecount-) container.
+  - `sarek` - the [sarek](#sarek-) container.
+  - `snpeffgrch37` - the [snpeffgrch37](#snpeffgrch37-) container.
+  - `snpeffgrch38` - the [snpeffgrch38](#snpeffgrch38-) container.
+  - `vepgrch37` - the [vepgrch37](#vepgrch37-) container.
+  - `vepgrch38` - the [vepgrch38](#vepgrch38-) container.
+
+- `--docker`: Build containers using `Docker`
+- `--push`: Push containers to `DockerHub`
+- `--repository`: Build containers under given repository.
+Default: `maxulysse`
+- `--singularity`: Build containers using `Singularity`.
+- `--containerPath`: Select where to download containers.
+Default: `$PWD`
+- `--tag`: Build containers using given tag.
+Default is version number.
+
+### Example
+
+```bash
+nextflow run buildContainers.nf --docker --singularity --push --containers sarek
+```
+
+### For lazy users
+We provide script to build/push or pull all containers
+```bash
+./scripts/do_all.sh        # Build all docker containers
+./scripts/do_all.sh --push # Build and push all Docker containers into DockerHub
+./scripts/do_all.sh --pull # Pull all containers from DockerHub with Singularity
+```
+
+## Building your own
+Most of the containers are designed using Bioconda.
+The `environment.yml` file can easilly be modified if particular versions of tools are more suited to your needs.
+You can then use the building script to build your own containers.
+You'll just need to specify the correct repository either in command line or in the configuration files.
 
 [allelecount-link]: https://github.com/cancerit/alleleCount
 [bcftools-link]: https://github.com/samtools/bcftools

scripts/do_all.sh

@@ -57,8 +57,7 @@ function toLower() {
 
 if [[ $TOOL = docker ]] && [[ GRCh37,GRCh38 =~ $GENOME ]]
 then
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers r-base,runallelecount,sarek,snpeff
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 else
     nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 fi