Merge pull request #403 from nf-core/update_sentieon_dnamodelapply

Replace local version of SENTIEON_DNAMODELAPPLY with nf-core version
nf-core · Aug 15, 2023 · bc20d53 · bc20d53
2 parents 383bb2d + c160035
commit bc20d53
Show file tree

Hide file tree

Showing 6 changed files with 167 additions and 52 deletions.
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
 - Installed the nf-core version of the sentieon/datametrics module [#400](https://github.com/nf-core/raredisease/pull/400)
 - Installed the nf-core version of the sentieon/dedup module. The dedup module also contains a call to Sentieon's LocusCollector [#401](https://github.com/nf-core/raredisease/pull/401)
 - Removing Sentieon-based BQSR. Recent Illumina sequencers tend to provide well-calibrated BQs, so BQSR may not provide much benefit [#402](https://github.com/nf-core/raredisease/pull/402)
+- Installed the nf-core version of the sentieon/dnamodelapply module [#403](https://github.com/nf-core/raredisease/pull/403)
 
 ### `Fixed`
 

diff --git a/modules.json b/modules.json
@@ -360,6 +360,11 @@
                         "git_sha": "915a0b16ba3e40ef59e7b44843b3118e17a9c906",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/dnamodelapply": {
+                        "branch": "master",
+                        "git_sha": "43ef68091a1188fd8dc4c03f9341b556803c7514",
+                        "installed_by": ["modules"]
+                    },
                     "sentieon/readwriter": {
                         "branch": "master",
                         "git_sha": "b28e4dde755117e8dab5d6e85e292f145b8b53c3",

diff --git a/modules/local/sentieon/dnamodelapply.nf b/modules/local/sentieon/dnamodelapply.nf
diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf
diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml
diff --git a/subworkflows/local/variant_calling/call_snv_sentieon.nf b/subworkflows/local/variant_calling/call_snv_sentieon.nf
@@ -3,7 +3,7 @@
 //
 
 include { SENTIEON_DNASCOPE                        } from '../../../modules/local/sentieon/dnascope'
-include { SENTIEON_DNAMODELAPPLY                   } from '../../../modules/local/sentieon/dnamodelapply'
+include { SENTIEON_DNAMODELAPPLY                   } from '../../../modules/nf-core/sentieon/dnamodelapply/main'
 include { BCFTOOLS_MERGE                           } from '../../../modules/nf-core/bcftools/merge/main'
 include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_SEN } from '../../../modules/nf-core/bcftools/norm/main'
 include { BCFTOOLS_NORM as REMOVE_DUPLICATES_SEN   } from '../../../modules/nf-core/bcftools/norm/main'
@@ -28,7 +28,7 @@ workflow CALL_SNV_SENTIEON {
 
         SENTIEON_DNASCOPE ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_dbsnp, ch_dbsnp_index, ch_call_interval, ch_ml_model )
 
-        SENTIEON_DNAMODELAPPLY ( SENTIEON_DNASCOPE.out.vcf_index, ch_genome_fasta, ch_genome_fai, ch_ml_model )
+        SENTIEON_DNAMODELAPPLY ( SENTIEON_DNASCOPE.out.vcf_index, ch_genome_fasta, ch_genome_fai, [ [:], ch_ml_model ] )
 
         BCF_FILTER_ONE (SENTIEON_DNAMODELAPPLY.out.vcf )