Improve tools schema validation

CHANGELOG.md

@@ -111,13 +111,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#592](https://github.com/nf-core/sarek/pull/592) - Fix optional resources for Mutect2, GetPileupSummaries, and HaplotypeCaller: issue [#299](https://github.com/nf-core/sarek/issues/299), [#359](https://github.com/nf-core/sarek/issues/359), [#367](https://github.com/nf-core/sarek/issues/367)
 - [#598](https://github.com/nf-core/sarek/pull/598), [#614](https://github.com/nf-core/sarek/pull/614), [#626](https://github.com/nf-core/sarek/pull/626) - Remove WARNING message for config selector not matching
 - [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for correct data type for `params.step`
-- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for no empty `--tools` with `--step variant_calling` or `--step annotation`
+- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for no empty `--tools` with `--step variant_calling` or `--step annotate`
 - [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
 - [#602](https://github.com/nf-core/sarek/pull/602) - Fixed bug in `alignment_to_fastq` and added tests
 - [#609](https://github.com/nf-core/sarek/pull/609) - Remove unused intervals code, reorganize combined intervals file
 - [#613](https://github.com/nf-core/sarek/pull/613) - Fixed filenames for `dbnsfp` and `SpliceAI` `VEP` plugin
 - [#615](https://github.com/nf-core/sarek/pull/615) - Fix ASCAT igenomes file paths
 - [#619](https://github.com/nf-core/sarek/pull/619) - Fix issue with checking samplesheet content with AWS
+- [#628](https://github.com/nf-core/sarek/pull/628) - Fix issue with value converting to string before schema validation
+- [#628](https://github.com/nf-core/sarek/pull/628) - Fix dbsnp check issue with `--step annotate`
 
 ### Deprecated
 

lib/WorkflowMain.groovy

@@ -82,13 +82,12 @@ class WorkflowMain {
     //
     // Get attribute from genome config file e.g. fasta
     //
-    public static String getGenomeAttribute(params, attribute) {
-        def val = ''
+    public static Object getGenomeAttribute(params, attribute) {
         if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
             if (params.genomes[ params.genome ].containsKey(attribute)) {
-                val = params.genomes[ params.genome ][ attribute ]
+                return params.genomes[ params.genome ][ attribute ]
             }
         }
-        return val
+        return null
     }
 }

subworkflows/local/prepare_genome.nf

@@ -62,34 +62,34 @@ workflow PREPARE_GENOME {
 
     // prepare ascat reference files
     allele_files = ascat_alleles
-    if( params.ascat_alleles.endsWith('.zip')){
+    if (params.ascat_alleles && params.ascat_alleles.endsWith('.zip')) {
         UNZIP_ALLELES(ascat_alleles.map{ it -> [[id:it[0].baseName], it] })
         allele_files = UNZIP_ALLELES.out.unzipped_archive.map{ it[1] }
         ch_versions = ch_versions.mix(UNZIP_ALLELES.out.versions)
     }
 
     loci_files = ascat_loci
-    if( params.ascat_loci.endsWith('.zip')){
+    if (params.ascat_loci && params.ascat_loci.endsWith('.zip')) {
         UNZIP_LOCI(ascat_loci.map{ it -> [[id:it[0].baseName], it] })
         loci_files = UNZIP_LOCI.out.unzipped_archive.map{ it[1] }
         ch_versions = ch_versions.mix(UNZIP_LOCI.out.versions)
     }
     gc_file = ascat_loci_gc
-    if( params.ascat_loci_gc.endsWith('.zip')){
+    if (params.ascat_loci_gc && params.ascat_loci_gc.endsWith('.zip')) {
         UNZIP_GC(ascat_loci_gc.map{ it -> [[id:it[0].baseName], it] })
         gc_file = UNZIP_GC.out.unzipped_archive.map{ it[1] }
         ch_versions = ch_versions.mix(UNZIP_GC.out.versions)
     }
     rt_file = ascat_loci_rt
-    if( params.ascat_loci_rt.endsWith('.zip')){
+    if (params.ascat_loci_rt && params.ascat_loci_rt.endsWith('.zip')) {
         UNZIP_RT(ascat_loci_rt.map{ it -> [[id:it[0].baseName], it] })
         rt_file = UNZIP_RT.out.unzipped_archive.map{ it[1] }
         ch_versions = ch_versions.mix(UNZIP_RT.out.versions)
     }
 
 
     chr_files = chr_dir
-    if ( params.chr_dir.endsWith('tar.gz')){
+    if (params.chr_dir && params.chr_dir.endsWith('tar.gz')) {
         UNTAR_CHR_DIR(chr_dir.map{ it -> [[id:it[0].baseName], it] })
         chr_files = UNTAR_CHR_DIR.out.untar.map{ it[1] }
         ch_versions = ch_versions.mix(UNTAR_CHR_DIR.out.versions)

workflows/sarek.nf

@@ -99,7 +99,7 @@ if(params.tools && params.tools.contains('mutect2')){
 // Fails when missing resources for baserecalibrator
 // Warns when missing resources for haplotypecaller
 if(!params.dbsnp && !params.known_indels){
-    if(!params.skip_tools || params.skip_tools && !params.skip_tools.contains('baserecalibrator')){
+    if (params.step in ['mapping', 'markduplicates', 'prepare_recalibration', 'recalibrate'] && (!params.skip_tools || (params.skip_tools && !params.skip_tools.contains('baserecalibrator')))){
         log.error "Base quality score recalibration requires at least one resource file. Please provide at least one of `--dbsnp` or `--known_indels`\nYou can skip this step in the workflow by adding `--skip_tools baserecalibrator` to the command."
         exit 1
     }