bring in changes from main

uclahs-cds · Jan 29, 2024 · 6560630 · 6560630
2 parents 30dfed1 + 1360225
commit 6560630
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Showing 4 changed files with 44 additions and 22 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,12 +8,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Changed
+- Pass reference index to `SomaticSniper` processes
 - Update GATK `v4.4.0.0` to `v4.5.0.0`
 
 ## [8.0.0-rc.1] - 2023-12-13
 
 ### Changed
 - `Strelka2` retry triggered by error code `1`
+- Use external `indexFile` function
+- Update submodules
 - Sample names sanitized for all output
 - Sample names parsed from input BAMs
 - Update `MuSE` to `v2.0.4`

diff --git a/main.nf b/main.nf
@@ -8,6 +8,7 @@ include { run_validate_PipeVal } from './external/pipeline-Nextflow-module/modul
         main_process: "./" //Save logs in <log_dir>/process-log/run_validate_PipeVal
         ]
     )
+include { indexFile } from './external/pipeline-Nextflow-module/modules/common/indexFile/main.nf'
 
 log.info """\
     ------------------------------------
@@ -106,19 +107,6 @@ include { intersect } from './module/intersect' addParams(
         params.sample_id,
         [:]))
 
-// Returns the index file for the given bam or vcf
-def indexFile(bam_or_vcf) {
-    if(bam_or_vcf.endsWith('.bam')) {
-        return "${bam_or_vcf}.bai"
-        }
-    else if(bam_or_vcf.endsWith('vcf.gz')) {
-        return "${bam_or_vcf}.tbi"
-        }
-    else {
-        throw new Exception("Index file for ${bam_or_vcf} file type not supported. Use .bam or .vcf.gz files.")
-        }
-    }
-
 Channel
     .from( params.samples_to_process )
         .filter{ it.sample_type == 'tumor' }

diff --git a/module/somaticsniper-processes.nf b/module/somaticsniper-processes.nf
@@ -24,6 +24,7 @@ process call_sSNV_SomaticSniper {
     path tumor
     path normal
     path reference
+    path reference_index
 
     output:
     path "*.vcf", emit: bam_somaticsniper
@@ -66,6 +67,7 @@ process convert_BAM2Pileup_SAMtools {
     input:
     tuple val(type), path(bam)
     path reference
+    path reference_index
 
     output:
     tuple val(type), path("${params.output_filename}_raw-${type}.pileup"), emit: raw_pileup
@@ -212,6 +214,7 @@ process generate_ReadCount_bam_readcount {
 
     input:
     path reference
+    path reference_index
     path site_list
     path tumor
     path tumor_index

diff --git a/module/somaticsniper.nf b/module/somaticsniper.nf
@@ -28,13 +28,23 @@ workflow somaticsniper {
     normal_index
 
     main:
-        call_sSNV_SomaticSniper(tumor_bam, normal_bam, params.reference)
+        call_sSNV_SomaticSniper(
+            tumor_bam,
+            normal_bam,
+            params.reference,
+            params.reference_index
+            )
         tumor_bam_path = tumor_bam
             .map{it -> ['tumor', it]}
         normal_bam_path = normal_bam
             .map{it -> ['normal', it]}
-        ch_convert_BAM2Pileup_SAMtools_bams = tumor_bam_path.mix(normal_bam_path)
-        convert_BAM2Pileup_SAMtools(ch_convert_BAM2Pileup_SAMtools_bams, params.reference)
+        ch_convert_BAM2Pileup_SAMtools_bams = tumor_bam_path
+            .mix(normal_bam_path)
+        convert_BAM2Pileup_SAMtools(
+            ch_convert_BAM2Pileup_SAMtools_bams,
+            params.reference,
+            params.reference_index
+            )
         create_IndelCandidate_SAMtools(convert_BAM2Pileup_SAMtools.out.raw_pileup)
 
         // tumor and normal need to be processed seperately.
@@ -47,12 +57,30 @@ workflow somaticsniper {
             }
             .set { ch_snpfilter }
 
-        apply_NormalIndelFilter_SomaticSniper(call_sSNV_SomaticSniper.out.bam_somaticsniper, ch_snpfilter.normal)
-        apply_TumorIndelFilter_SomaticSniper(apply_NormalIndelFilter_SomaticSniper.out.vcf_normal, ch_snpfilter.tumor)
-        create_ReadCountPosition_SomaticSniper(apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor)
-        generate_ReadCount_bam_readcount(params.reference,create_ReadCountPosition_SomaticSniper.out.snp_positions, tumor_bam, tumor_index)
-        filter_FalsePositive_SomaticSniper(apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor, generate_ReadCount_bam_readcount.out.readcount)
-        call_HighConfidenceSNV_SomaticSniper(filter_FalsePositive_SomaticSniper.out.fp_pass)
+        apply_NormalIndelFilter_SomaticSniper(
+            call_sSNV_SomaticSniper.out.bam_somaticsniper,
+            ch_snpfilter.normal
+            )
+        apply_TumorIndelFilter_SomaticSniper(
+            apply_NormalIndelFilter_SomaticSniper.out.vcf_normal,
+            ch_snpfilter.tumor
+            )
+        create_ReadCountPosition_SomaticSniper(
+            apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor
+            )
+        generate_ReadCount_bam_readcount(
+            params.reference,
+            params.reference_index,
+            create_ReadCountPosition_SomaticSniper.out.snp_positions,
+            tumor_bam,tumor_index
+            )
+        filter_FalsePositive_SomaticSniper(
+            apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor,
+            generate_ReadCount_bam_readcount.out.readcount
+            )
+        call_HighConfidenceSNV_SomaticSniper(
+            filter_FalsePositive_SomaticSniper.out.fp_pass
+            )
         // combining to delay compression until after filtering step
         compress_file_bzip2(
             generate_ReadCount_bam_readcount.out.readcount