Merge pull request #721 from MaxUlysse/COSMIC

Completly remove COSMIC

Author: Szilveszter Juhos

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Removed`
 -   [#715](https://github.com/SciLifeLab/Sarek/pull/715) - Remove `defReferencesFiles` function from `buildReferences.nf`
+-   [#721](https://github.com/SciLifeLab/Sarek/pull/721) - Remove COSMIC docs
 
 ## [2.2.2] - 2018-12-19
 

docs/PARAMETERS.md

@@ -64,11 +64,11 @@ Only required if you use the awsbatch profile. This parameter specifies the queu
 
 ### --awsqueue_tiny `BatchQueueName`
 
-Only used if you use the awsbatch profile. This parameter specifies a queue used for certain small jobs that might still require a significant amount of disk storage. 
+Only used if you use the awsbatch profile. This parameter specifies a queue used for certain small jobs that might still require a significant amount of disk storage.
 
 ### --localReportDir `Directory`
 
-Only used if you use the awsbatch profile. This parameter specifies an output directory for nextflow reports, such as Sarek_timeline.html, which currently is not fully supported to store on s3. 
+Only used if you use the awsbatch profile. This parameter specifies an output directory for nextflow reports, such as Sarek_timeline.html, which currently is not fully supported to store on s3.
 
 ### --verbose
 
@@ -132,10 +132,6 @@ However, if needed, you can specify any reference file at the command line.
 
 ### --bwaIndex `bwaIndex file`
 
-### --cosmic `cosmic file`
-
-### --cosmicIndex `cosmicIndex file`
-
 ### --dbsnp `dbsnp file`
 
 ### --dbsnpIndex `dbsnpIndex file`

docs/REFERENCES.md

@@ -27,8 +27,6 @@ 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.
@@ -69,31 +67,6 @@ bwa index -6 Homo_sapiens_assembly38.fasta
 
 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.
-
-## COSMIC files
-
-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.
-
-Example:
-
-```bash
-samtools faidx human_g1k_v37_decoy.fasta
-sh Create_Cosmic.sh human_g1k_v37_decoy.fasta.fai
-```
-
-Note: CosmicCodingMuts.vcf.gz & CosmicNonCodingVariants.vcf.gz must be in same folder as Create\_Cosmic.sh when executed.
-
-To index the resulting VCF file use [igvtools](https://software.broadinstitute.org/software/igv/igvtools).
-
-```bash
-igvtools index <cosmicvxx.vcf>
-```
-
 ## smallGRCh37
 
 Use `--genome smallGRCh37` to map against a small reference genome based on GRCh37.