update docs [skip ci]

Author: maxulysse

CHANGELOG.md

@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#671](https://github.com/SciLifeLab/Sarek/pull/671) - New `publishDirMode` param and docs
 -   [#673](https://github.com/SciLifeLab/Sarek/pull/673), [#675](https://github.com/SciLifeLab/Sarek/pull/675),  [#676](https://github.com/SciLifeLab/Sarek/pull/676) - Profiles for BinAC and CFC clusters in Tübingen
 -   [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Add container for `CreateIntervalBeds`
--   [#692](https://github.com/SciLifeLab/Sarek/pull/692) - Add AWS iGenomes possibilities (currently under `iGRCh37` and `iGRCh38`)
+-   [#692](https://github.com/SciLifeLab/Sarek/pull/692), [#697](https://github.com/SciLifeLab/Sarek/pull/697) - Add AWS iGenomes possibilities (within `conf/igenomes.conf`)
 -   [#694](https://github.com/SciLifeLab/Sarek/pull/694) - Add monochrome and grey logos for light or dark background
 
 ### `Changed`

conf/genomes.config

@@ -4,10 +4,12 @@
  * -------------------------------------------------
  * Path to reference files
  * -------------------------------------------------
- * Imported under all Nextflow profiles in
+ * Imported under Nextflow profiles in
  * nextflow.config
  * -------------------------------------------------
- * Modify to add specific versions of genomes
+ * Defines reference genomes, using paths
+ * Can be used by any config that customises the base
+ * path using $params.genome_base / --genome_base
  * -------------------------------------------------
  */
 

conf/igenomes.config

@@ -2,12 +2,14 @@
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------
- * Path to reference files
+ * Path to iGenomes reference files
  * -------------------------------------------------
- * Imported under all Nextflow profiles in
+ * Imported under Nextflow profiles in
  * nextflow.config
  * -------------------------------------------------
- * Modify to add specific versions of genomes
+ * Defines reference genomes, using iGenome paths
+ * Can be used by any config that customises the base
+ * path using $params.genome_base / --genome_base
  * -------------------------------------------------
  */
 

docs/REFERENCES.md

@@ -1,11 +1,13 @@
 # Genomes and reference files
 
-Sarek currently uses GRCh38 by default. The settings are in `genomes.config`, they can be tailored to your needs.
+Sarek currently uses GRCh38 by default.
+The settings are in `genomes.config`, they can be tailored to your needs.
 The [`buildReferences.nf`](#buildreferencesnf) script is used to build the indexes for the reference test.
 
 ## GRCh37
 
-Use `--genome GRCh37` to map against GRCh37. Before doing so and if you are not on UPPMAX, you need to adjust the settings in `genomes.config` to your needs.
+Use `--genome GRCh37` to map against GRCh37.
+Before doing so and if you are not on UPPMAX, you need to adjust the settings in `genomes.config` to your needs.
 
 ### GATK bundle
 
@@ -20,21 +22,27 @@ The following files need to be downloaded:
 
 ### Other files for GRCh37
 
-From our repo, get the [`intervals` list file](https://raw.githubusercontent.com/SciLifeLab/Sarek/master/repeats/wgs_calling_regions.grch37.list). More information about this file in the [intervals documentation](INTERVALS.md)
+From our repo, get the [`intervals` list file](https://raw.githubusercontent.com/SciLifeLab/Sarek/master/repeats/wgs_calling_regions.grch37.list).
+More information about this file in the [intervals documentation](INTERVALS.md)
 
 Description of how to generate the Loci file used in the ASCAT process is described [here](https://github.com/SciLifeLab/Sarek/blob/master/docs/ASCAT.md).
 
 You can create your own cosmic reference for any human reference as specified below in the Cosmic section.
 
 ## GRCh38
 
-Use `--genome GRCh38` to map against GRCh38. Before doing so and if you are not on UPPMAX, you need to adjust the settings in `genomes.config` to your needs.
+Use `--genome GRCh38` to map against GRCh38.
+Before doing so and if you are not on UPPMAX, you need to adjust the settings in `genomes.config` to your needs.
 
-To get the needed files, download the GATK bundle for GRCh38 from [ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/](ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/). You can also download the required files from the Google Cloud mirror link [here](https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0).
+To get the needed files, download the GATK bundle for GRCh38 from [ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/](ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/).
+You can also download the required files from the Google Cloud mirror link [here](https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0).
 
 The MD5SUM of `Homo_sapiens_assembly38.fasta` included in that file is 7ff134953dcca8c8997453bbb80b6b5e.
 
-If you download the data from the FTP servers `beta/` directory, which seems to be an older version of the bundle, only `Homo_sapiens_assembly38.known_indels.vcf` is needed. Also, you can omit `dbsnp_138_` and `dbsnp_144` files as we use `dbsnp_146`. The old ones also use the wrong chromosome naming convention. The Google Cloud mirror has all data in the `v0` directory, but requires you to remove the `resources_broad_hg38_v0_` prefixes from all files.
+If you download the data from the FTP servers `beta/` directory, which seems to be an older version of the bundle, only `Homo_sapiens_assembly38.known_indels.vcf` is needed.
+Also, you can omit `dbsnp_138_` and `dbsnp_144` files as we use `dbsnp_146`.
+The old ones also use the wrong chromosome naming convention.
+The Google Cloud mirror has all data in the `v0` directory, but requires you to remove the `resources_broad_hg38_v0_` prefixes from all files.
 
 The following files need to be downloaded:
 
@@ -68,7 +76,8 @@ You can create your own cosmic reference for any human reference as specified be
 To annotate with COSMIC variants during MuTect1/2 Variant Calling you need to create a compatible VCF file.
 Download the coding and non-coding VCF files from [COSMIC](http://cancer.sanger.ac.uk/cosmic/download) and
 process them with the [Create\_Cosmic.sh](https://github.com/SciLifeLab/Sarek/tree/master/scripts/Create_Cosmic.sh)
-script for either GRCh37 or GRCh38. The script requires a fasta index `.fai`, of the reference file you are using.
+script for either GRCh37 or GRCh38.
+The script requires a fasta index `.fai`, of the reference file you are using.
 
 Example:
 
@@ -87,11 +96,12 @@ igvtools index <cosmicvxx.vcf>
 
 ## smallGRCh37
 
-Use `--genome smallGRCh37` to map against a small reference genome based on GRCh37. `smallGRCh37` is the default genome for the testing profile (`-profile testing`).
+Use `--genome smallGRCh37` to map against a small reference genome based on GRCh37.
+`smallGRCh37` is the default genome for the testing profile (`-profile testing`).
 
 ## AWS iGenomes
 Sarek is using [AWS iGenomes](https://ewels.github.io/AWS-iGenomes/), which facilitate storing and sharing references.
-Both `GRCh37` and `GRCh38` are available with `--genome iGRCh37` or `--genome iGRCh38` respectively, it contains all data previously detailed.
+Both `GRCh37` and `GRCh38` are available with `--genome GRCh37` or `--genome GRCh38` respectively with any profile using the `conf/igenomes.config` file (eg.: `awsbatch`), or you can specify it with `-c conf/igenomes.config`, it contains all data previously detailed.
 
 ## buildReferences.nf