More input checks

CHANGELOG.md

@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#733](https://github.com/nf-core/sarek/pull/733) - Add description for params.cf_chrom_len
 - [#734](https://github.com/nf-core/sarek/pull/734) - nf-core modules update -a
 - [#736](https://github.com/nf-core/sarek/pull/736) - More extensive CI for default test
+- [#742](https://github.com/nf-core/sarek/pull/742) - Requiring the Hyplotypecaller to be specified as one of the tools for joint germline genotyping.
 
 ### Fixed
 
@@ -47,6 +48,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Deprecated
 
 ### Removed
+- [#742](https://github.com/nf-core/sarek/pull/742) - Removed some lines from the usage-doc as Sarek no longer support input supplied as a list of multiple csv-files.
+
 
 ## [3.0.1](https://github.com/nf-core/sarek/releases/tag/3.0.1) - Saiva
 

docs/usage.md

@@ -44,12 +44,6 @@ If multiple samples IDs are specified in the CSV file, Sarek will consider all f
 
 Output from Variant Calling and/or Annotation will be in a specific directory for each sample and tool configuration (or normal/tumor pair if applicable).
 
-Multiple CSV files can be specified if the path is enclosed in quotes.
-
-```bash
---input '[path to sample sheet file(s)]'
-```
-
 ### Overview: Samplesheet Columns
 
 | Column    | Description                                                                                                                                                                                                                                                                                                                       |

workflows/sarek.nf

@@ -114,6 +114,10 @@ if(!params.dbsnp && !params.known_indels){
 
     }
 }
+if (params.joint_germline && (!params.tools || !params.tools.split(',').contains('haplotypecaller'))){
+    log.error "The Haplotypecaller should be specified as one of the tools when doing joint germline variant calling. (The Haplotypecaller could be specified by adding `--tools haplotypecaller` to the nextflow command.) "
+    exit 1
+}
 if (params.joint_germline && (!params.dbsnp || !params.known_indels || !params.known_snps || params.no_intervals)){
     log.warn "If Haplotypecaller is specified, without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \nJoint germline variant calling also requires intervals in order to genotype the samples. As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed."
 }