Merge pull request nf-core#1488 from asp8200/fixing_test_full_germline

Fixing call to GATK4_HAPLOTYPECALLER
asp8200 · Apr 29, 2024 · 3fd2743 · 3fd2743
2 parents 502b6de + eaa1373
commit 3fd2743
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix
+- [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline`
 
 ### Removed
 

diff --git a/main.nf b/main.nf
@@ -177,12 +177,12 @@ workflow NFCORE_SAREK {
     rt_file                = PREPARE_GENOME.out.rt_file
 
     // Tabix indexed vcf files
-    bcftools_annotations_tbi  = params.bcftools_annotations    ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi)   : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
-    dbsnp_tbi                 = params.dbsnp                   ? params.dbsnp_tbi                ? Channel.fromPath(params.dbsnp_tbi)                  : PREPARE_GENOME.out.dbsnp_tbi                : Channel.value([])
-    germline_resource_tbi     = params.germline_resource       ? params.germline_resource_tbi    ? Channel.fromPath(params.germline_resource_tbi)      : PREPARE_GENOME.out.germline_resource_tbi    : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
-    known_indels_tbi          = params.known_indels            ? params.known_indels_tbi         ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi         : Channel.value([])
-    known_snps_tbi            = params.known_snps              ? params.known_snps_tbi           ? Channel.fromPath(params.known_snps_tbi)             : PREPARE_GENOME.out.known_snps_tbi           : Channel.value([])
-    pon_tbi                   = params.pon                     ? params.pon_tbi                  ? Channel.fromPath(params.pon_tbi)                    : PREPARE_GENOME.out.pon_tbi                  : Channel.value([])
+    bcftools_annotations_tbi  = params.bcftools_annotations    ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
+    dbsnp_tbi                 = params.dbsnp                   ? params.dbsnp_tbi                ? Channel.fromPath(params.dbsnp_tbi).collect()                : PREPARE_GENOME.out.dbsnp_tbi                : Channel.value([])
+    germline_resource_tbi     = params.germline_resource       ? params.germline_resource_tbi    ? Channel.fromPath(params.germline_resource_tbi).collect()    : PREPARE_GENOME.out.germline_resource_tbi    : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
+    known_indels_tbi          = params.known_indels            ? params.known_indels_tbi         ? Channel.fromPath(params.known_indels_tbi).collect()         : PREPARE_GENOME.out.known_indels_tbi         : Channel.value([])
+    known_snps_tbi            = params.known_snps              ? params.known_snps_tbi           ? Channel.fromPath(params.known_snps_tbi).collect()           : PREPARE_GENOME.out.known_snps_tbi           : Channel.value([])
+    pon_tbi                   = params.pon                     ? params.pon_tbi                  ? Channel.fromPath(params.pon_tbi).collect()                  : PREPARE_GENOME.out.pon_tbi                  : Channel.value([])
 
     // known_sites is made by grouping both the dbsnp and the known snps/indels resources
     // Which can either or both be optional