Merge pull request #406 from genomic-medicine-sweden/dnascope

Add sentieon/dnascope from nf-core/modules
nf-core · Aug 18, 2023 · e58c7ef · e58c7ef
2 parents cf78b22 + 2f47cd1
commit e58c7ef
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Showing 8 changed files with 213 additions and 72 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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)
 - Installed the nf-core version of the sentieon/wgsmetricsalgo module [#404](https://github.com/nf-core/raredisease/pull/404)
+- Installed the nf-core version of the sentieon/dnascope module [#406](https://github.com/nf-core/raredisease/pull/406)
 
 ### `Fixed`
 

diff --git a/conf/modules/align_sentieon.config b/conf/modules/align_sentieon.config
@@ -37,6 +37,7 @@ process {
     withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
         ext.args = { $params.rmdup ? "--rmdup" : '' }
         ext.prefix = { "${meta.id}_dedup" }
+        ext.suffix = ".bam"
         publishDir = [
             enabled: !params.save_mapped_as_cram,
             path: { "${params.outdir}/alignment" },

diff --git a/modules.json b/modules.json
@@ -365,6 +365,11 @@
                         "git_sha": "43ef68091a1188fd8dc4c03f9341b556803c7514",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/dnascope": {
+                        "branch": "master",
+                        "git_sha": "127edadc279e19da093fdd513926c6cdee82c306",
+                        "installed_by": ["modules"]
+                    },
                     "sentieon/readwriter": {
                         "branch": "master",
                         "git_sha": "b28e4dde755117e8dab5d6e85e292f145b8b53c3",

diff --git a/modules/local/sentieon/dnascope.nf b/modules/local/sentieon/dnascope.nf
diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf
diff --git a/modules/nf-core/sentieon/dnascope/meta.yml b/modules/nf-core/sentieon/dnascope/meta.yml
diff --git a/subworkflows/local/variant_calling/call_snv_sentieon.nf b/subworkflows/local/variant_calling/call_snv_sentieon.nf
@@ -2,7 +2,7 @@
 // A subworkflow to call SNVs by sentieon dnascope with a machine learning model.
 //
 
-include { SENTIEON_DNASCOPE                        } from '../../../modules/local/sentieon/dnascope'
+include { SENTIEON_DNASCOPE                        } from '../../../modules/nf-core/sentieon/dnascope/main'
 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'
@@ -15,20 +15,22 @@ include { BCFTOOLS_FILTER as BCF_FILTER_TWO        } from '../../../modules/nf-c
 workflow CALL_SNV_SENTIEON {
     take:
         ch_bam_bai       // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
-        ch_genome_fasta  // channel: [mandatory] [ path(fasta) ]
-        ch_genome_fai    // channel: [mandatory] [ path(fai) ]
+        ch_genome_fasta  // channel: [mandatory] [ val(meta), path(fasta) ]
+        ch_genome_fai    // channel: [mandatory] [ val(meta), path(fai) ]
         ch_dbsnp         // channel: [mandatory] [ val(meta), path(vcf) ]
         ch_dbsnp_index   // channel: [mandatory] [ val(meta), path(tbi) ]
-        ch_call_interval // channel: [mandatory] [ path(interval) ]
-        ch_ml_model      // channel: [mandatory] [ path(model) ]
+        ch_call_interval // channel: [mandatory] [ val(meta), path(interval) ]
+        ch_ml_model      // channel: [mandatory] [ val(meta), path(model) ]
         ch_case_info     // channel: [mandatory] [ val(case_info) ]
 
     main:
         ch_versions = Channel.empty()
 
         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 ] )
+        ch_dnamodelapply_in = SENTIEON_DNASCOPE.out.vcf.join(SENTIEON_DNASCOPE.out.index)
+
+        SENTIEON_DNAMODELAPPLY ( ch_dnamodelapply_in, ch_genome_fasta, ch_genome_fai, ch_ml_model )
 
         BCF_FILTER_ONE (SENTIEON_DNAMODELAPPLY.out.vcf )
 

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -209,8 +209,8 @@ workflow RAREDISEASE {
     ch_cadd_header              = Channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect()
     ch_cadd_resources           = params.cadd_resources                    ? Channel.fromPath(params.cadd_resources).collect()
                                                                            : Channel.value([])
-    ch_call_interval            = params.call_interval                     ? Channel.fromPath(params.call_interval).collect()
-                                                                           : Channel.value([])
+    ch_call_interval            = params.call_interval                     ? Channel.fromPath(params.call_interval).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                                           : Channel.value([[:],[]])
     ch_dbsnp_tbi                = params.known_dbsnp_tbi                   ? Channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it[0].simpleName], it]}.collect()
                                                                            : ch_references.known_dbsnp_tbi.ifEmpty([[],[]])
     ch_gcnvcaller_model         = params.gcnvcaller_model                  ? Channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true )
@@ -234,8 +234,8 @@ workflow RAREDISEASE {
                                                                            : Channel.empty()
     ch_intervals_y              = params.intervals_y                       ? Channel.fromPath(params.intervals_y).collect()
                                                                            : Channel.empty()
-    ch_ml_model                 = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).collect()
-                                                                           : Channel.value([])
+    ch_ml_model                 = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                                           : Channel.value([[:],[]])
     ch_mt_intervals             = ch_references.mt_intervals
     ch_mtshift_backchain        = ch_references.mtshift_backchain
     ch_mtshift_bwaindex         = ch_references.mtshift_bwa_index