Fix Sentieon

CHANGELOG.md

@@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet
 - [1743](https://github.com/nf-core/sarek/pull/1743) - Add setup java 17 in GHA for latest Nextflow version
 - [1745](https://github.com/nf-core/sarek/pull/1745) - Fix bug where workflow can hang if the email parameter is set
+- [](https://github.com/nf-core/sarek/pull/) - Fix Sentieon module inputs
 
 ### Removed
 

conf/modules/aligner.config

@@ -30,11 +30,11 @@ process {
         }
 
         withName: 'SENTIEON_BWAMEM' {
+            ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]).concat('.bam') : "${meta.id}.sorted.bam" }
             ext.when   = { params.aligner == 'sentieon-bwamem' }
         }
 
         withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM' {
-            ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/preprocessing/" },
@@ -56,6 +56,7 @@ process {
         }
 
         withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN' {
+            ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
             // Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
             // However if it's skipped, reads need to be coordinate-sorted
             // Only name sort if Spark for Markduplicates + duplicate marking is not skipped

conf/modules/sentieon_dedup.config

@@ -16,7 +16,7 @@
 process {
 
     withName: 'SENTIEON_DEDUP' {
-        ext.prefix       = { "${meta.id}.dedup" }
+        ext.prefix       = { "${meta.id}.dedup.cram" }
         ext.when         = { params.tools && params.tools.split(',').contains('sentieon_dedup') }
         publishDir       = [
             [

subworkflows/local/bam_joint_calling_germline_sentieon/main.nf

@@ -36,7 +36,7 @@ workflow BAM_JOINT_CALLING_GERMLINE_SENTIEON {
         .map{ meta, gvcf, tbi, intervals -> [ [ id:'joint_variant_calling', intervals_name:intervals.baseName, num_intervals:meta.num_intervals ], gvcf, tbi, intervals ] }
         .groupTuple(by:[0, 3])
 
-    SENTIEON_GVCFTYPER(sentieon_input, fasta.map{meta, it -> [ it ]}, fai.map{meta, it -> [ it ]}, dbsnp, dbsnp_tbi)
+    SENTIEON_GVCFTYPER(sentieon_input, fasta, fai, dbsnp, dbsnp_tbi)
 
     BCFTOOLS_SORT(SENTIEON_GVCFTYPER.out.vcf_gz)
 

subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf

@@ -48,9 +48,9 @@ workflow BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER {
     emit_vcf = lst.size() > 0 ? lst[0] : ''
 
     SENTIEON_HAPLOTYPER(
-        cram_intervals_for_sentieon,
-        fasta.map{ meta, it -> it },
-        fasta_fai.map{ meta, it ->  it },
+        cram_intervals_for_sentieon.map{ meta, cram, crai, intervals, num_intervals -> [ meta, cram, crai, intervals, [] ]},
+        fasta,
+        fasta_fai,
         dbsnp,
         dbsnp_tbi,
         emit_vcf,