Update testing sample for v6.0.0-rc.1 (#170)

* Switch align-DNA test to Illumina sample * Update BAM2FASTQ test * Update sample for recalibrate-BAM * Update sample for calculate-targeted-coverage * Update tests for call-gSNP and call-sSNV * Update samples for call-gSNP and call-sSNV * Update sample for call-mtSNV * Update sample for call-gSV * Update sample for call-sSV * Update test cases * Update sample for sCNA * Update metapipeline_dna.nf test * Add sCNA assertion back * Update BAM entry batch test * Update FASTQ input test * Update CHANGELOG * Update nextflow.config * Update to common paths
uclahs-cds · Mar 12, 2024 · b8a6347 · b8a6347
1 parent b290629
commit b8a6347
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Showing 22 changed files with 236 additions and 246 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [6.0.0-rc.1] - 2024-03-11
 ### Added
 + pipeline-call-sCNA `v3.0.0` and its NFTest
 + Targeted coverage pipeline
@@ -18,6 +22,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 + Sanitize metadata passed to align-DNA
 + Calculate-targeted-coverage: update name from targeted-coverage
 + Save logs and input files for all pipelines
++ Update test samples
 
 ---
 

diff --git a/module/call_sSV/create_YAML_call_sSV.nf b/module/call_sSV/create_YAML_call_sSV.nf
@@ -9,11 +9,6 @@ import org.yaml.snakeyaml.Yaml
 *   @return A path to the input YAML
 */
 process create_YAML_call_sSV {
-    publishDir path: "${params.log_output_dir}/process-log",
-        mode: "copy",
-        pattern: ".command.*",
-        saveAs: { "${task.process}-${tumor_id}/log${file(it).getName()}" }
-
     publishDir "${params.output_dir}/intermediate/${task.process.replace(':', '/')}-${tumor_id}",
         pattern: 'call_sSV_input.yaml',
         mode: 'copy'

diff --git a/nextflow.config b/nextflow.config
@@ -1,7 +1,7 @@
 // Metadata
 manifest {
     name = 'metapipeline-DNA'
-    author = ['Yash Patel', 'Chenghao Zhu', 'Helena Winata', 'Alfredo Enrique Gonzalez', 'Nicholas Wang', 'Mohammed Faizal Eeman Mootor']
+    author = ['Yash Patel', 'Chenghao Zhu', 'Helena Winata', 'Alfredo Enrique Gonzalez', 'Nicholas Wang', 'Sorel Fitz-Gibbon', 'Mohammed Faizal Eeman Mootor', 'Nicole Zeltser']
     description = 'Nextflow pipeline to convert BAM to FASTQ, align, call gSNP, call sSNV, call gSV, call sSV and call mtSNV'
-    version = '5.3.1'
+    version = '6.0.0-rc.1'
 }
diff --git a/nftest.yaml b/nftest.yaml
diff --git a/test/test-align-DNA/test.config b/test/test-align-DNA/test.config
@@ -1,8 +1,8 @@
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'GZLUCPTA000001'
-    project_id = 'LUAD0000034'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'paired'
     override_realignment = false
 
@@ -26,36 +26,36 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-align-DNA"
 
     params.sample_data = [
-        'TCEB1-RCC-S00-9422T-027-166': [
-            'patient': 'TCEB1',
+        'NA24143': [
+            'patient': 'IlluminaPatient1',
             'state': 'tumor',
             'align-DNA': ['BWA-MEM2': ['BAM':'']],
             'original_data': [[
-                'read_group_identifier': 'S00-9422T_027_166.Seq1',
-                'sequencing_center': 'S00-9422T_027_166_NoIndex',
-                'library_identifier': 'S00-9422T_027_166_NoIndex',
-                'platform_technology': 'ILLUMINA',
-                'platform_unit': 'S00-9422T_027_166_NoIndex_L003',
-                'bam_header_sm': 'S00-9422T_027_166',
-                'lane': 0,
-                'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422T_027_166/collated_S00-9422T_027_166.Seq1_R1.fq.gz',
-                'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422T_027_166/collated_S00-9422T_027_166.Seq1_R2.fq.gz'
+                'read_group_identifier': 'NA24143RG',
+                'sequencing_center': 'Illumina',
+                'library_identifier': 'NA24143LIB',
+                'platform_technology': 'Illumina',
+                'platform_unit': 'Platform1',
+                'bam_header_sm': 'NA24143',
+                'lane': 1,
+                'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24143/IDPE2plus-NA24143-R4-MitoEx-1to100_S21_L001_R1_001.fastq.gz',
+                'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24143/IDPE2plus-NA24143-R4-MitoEx-1to100_S21_L001_R2_001.fastq.gz'
             ]]
         ],
-        'TCEB1-RCC-S00-9422N-079-114': [
-            'patient': 'TCEB1',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
             'align-DNA': ['BWA-MEM2': ['BAM':'']],
             'original_data': [[
-                'read_group_identifier': 'S00-9422N_079_114.Seq1',
-                'sequencing_center': 'S00-9422N_079_114_NoIndex',
-                'library_identifier': 'S00-9422N_079_114_NoIndex',
-                'platform_technology': 'ILLUMINA',
-                'platform_unit': 'S00-9422N_079_114_NoIndex_L003',
-                'bam_header_sm': 'S00-9422N_079_114',
-                'lane': 0,
-                'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422N_079_114/collated_S00-9422N_079_114.Seq1_R1.fq.gz',
-                'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/S00-9422N_079_114/collated_S00-9422N_079_114.Seq1_R2.fq.gz'
+                'read_group_identifier': 'NA24149RG',
+                'sequencing_center': 'Illumina',
+                'library_identifier': 'NA24149LIB',
+                'platform_technology': 'Illumina',
+                'platform_unit': 'Platform1',
+                'bam_header_sm': 'NA24149',
+                'lane': 1,
+                'read1_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24149/IDPE2plus-NA24149-R3-MitoEx-1to1000_S41_L001_R1_001.fastq.gz',
+                'read2_fastq': '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/FASTQ/NA24149/IDPE2plus-NA24149-R3-MitoEx-1to1000_S41_L001_R2_001.fastq.gz'
             ]]
         ]
     ]

diff --git a/test/test-bam2fastq/input.csv b/test/test-bam2fastq/input.csv
@@ -1,2 +1,2 @@
 patient,sample,state,bam
-TCEB1,TCEB1_RCC_S00-9422N_079_114,normal,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/bam2fastq/inputs/TCEB1_RCC_S00-9422N_079_114_merged_05prcnt.bam
+IlluminaPatient1,NA24149,normal,/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_IlluminaSampleTest_NA24149.bam
diff --git a/test/test-bam2fastq/test.config b/test/test-bam2fastq/test.config
@@ -2,8 +2,8 @@ params {
     input_csv = "${launchDir}/test/test-bam2fastq/input.csv"
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'GZLUCPTA000001'
-    project_id = 'LUAD0000034'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'paired'
     override_realignment = false
 
@@ -24,7 +24,7 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-convert-BAM2FASTQ"
 
     params.sample_data = [
-        'TCEB1_RCC_S00-9422N_079_114': [
+        'NA24149': [
             'convert-BAM2FASTQ': []
         ]
     ]

diff --git a/test/test-calculate-targeted-coverage/test.config b/test/test-calculate-targeted-coverage/test.config
@@ -3,8 +3,8 @@ import nextflow.util.SysHelper
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'TCEB1'
-    project_id = 'test'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'single'
 
     calculate_targeted_coverage {
@@ -30,10 +30,10 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-calculate-targeted-coverage"
 
     params.sample_data = [
-        '9422N': [
-            'patient': 'TCEB1_RCC_S00',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422N-079-114.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':'']
         ]
     ]
 

diff --git a/test/test-call-gSNP/test.config b/test/test-call-gSNP/test.config
@@ -3,8 +3,8 @@ import nextflow.util.SysHelper
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'TCEB1'
-    project_id = 'test'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'paired'
 
     call_gSNP {
@@ -28,15 +28,15 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-gSNP"
 
     params.sample_data = [
-        '9422T': [
-            'patient': 'TCEB1_RCC_S00',
+        'NA24143': [
+            'patient': 'IlluminaPatient1',
             'state': 'tumor',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422T_027_166.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':'']
         ],
-        '9422N': [
-            'patient': 'TCEB1_RCC_S00',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/meta-germline-somatic/systematic_tests/call-gSNP/inputs/TCEB1/TCEB1_RCC_S00-9422N-079-114.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':'']
         ]
     ]
 

diff --git a/test/test-call-gSV/test.config b/test/test-call-gSV/test.config
@@ -1,15 +1,16 @@
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'GZLUCPTA000001'
-    project_id = 'LUAD0000034'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'paired'
 
     call_gSV {
         subworkflow_cpus = 8
-        reference_fasta = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/downsampled_data/genome/genome.fa'
+        reference_fasta = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
         exclusion_file = '/hot/ref/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv'
         mappability_map = '/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz'
+        run_delly = false
     }
 
     arg_map = [:]
@@ -22,15 +23,15 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-gSV"
 
     params.sample_data = [
-        'GZLUCPTA000001-T001-P01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24143': [
+            'patient': 'IlluminaPatient1',
             'state': 'tumor',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':'']
         ],
-        'GZLUCPTA000001-N001-B01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':'']
         ]
     ]
 

diff --git a/test/test-call-mtSNV/test.config b/test/test-call-mtSNV/test.config
@@ -1,8 +1,8 @@
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'GZLUCPTA000001'
-    project_id = 'LUAD0000034'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'paired'
 
     call_mtSNV {
@@ -21,15 +21,15 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-mtSNV"
 
     params.sample_data = [
-        'GZLUCPTA000001-T001-P01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24143': [
+            'patient': 'IlluminaPatient1',
             'state': 'tumor',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':'']
         ],
-        'GZLUCPTA000001-N001-B01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':'']
         ]
     ]
 

diff --git a/test/test-call-sCNA/test-cnv_facets.config b/test/test-call-sCNA/test-cnv_facets.config
@@ -1,8 +1,8 @@
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'GZLUCPTA000001'
-    project_id = 'LUAD0000034'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'paired'
 
     call_sCNA {
@@ -25,15 +25,15 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-sCNA"
 
     params.sample_data = [
-        'GZLUCPTA000001-T001-P01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24143': [
+            'patient': 'IlluminaPatient1',
             'state': 'tumor',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':'']
         ],
-        'GZLUCPTA000001-N001-B01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':'']
         ]
     ]
 

diff --git a/test/test-call-sSNV/test.config b/test/test-call-sSNV/test.config
@@ -1,15 +1,15 @@
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'GZLUCPTA000001'
-    project_id = 'LUAD0000034'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
 
     sample_mode = 'paired'
 
     call_sSNV {
         subworkflow_cpus = 8
         algorithm = ['somaticsniper', 'strelka2', 'mutect2', 'muse']
-        reference = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/downsampled_data/genome/genome.fa'
+        reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
         exome = false
         intersect_regions = "${launchDir}/test/test-call-sSNV/Homo_sapiens_assembly38_no-decoy_downsampled.bed.gz"
         germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
@@ -27,15 +27,15 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-sSNV"
 
     params.sample_data = [
-        'GZLUCPTA000001-T001-P01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24143': [
+            'patient': 'IlluminaPatient1',
             'state': 'tumor',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':'']
         ],
-        'GZLUCPTA000001-N001-B01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':'']
         ]
     ]
 

diff --git a/test/test-call-sSV/test.config b/test/test-call-sSV/test.config
@@ -1,13 +1,13 @@
 params {
     work_dir = '/scratch/\$SLURM_JOB_ID'
     save_intermediate_files = true
-    patient = 'GZLUCPTA000001'
-    project_id = 'LUAD0000034'
+    patient = 'IlluminaPatient1'
+    project_id = 'IlluminaTest'
     sample_mode = 'paired'
 
     call_sSV {
         subworkflow_cpus = 8
-        reference_fasta = '/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/downsampled_data/genome/genome.fa'
+        reference_fasta = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
         algorithm = ['delly', 'manta']
         exclusion_file = '/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv'
     }
@@ -22,15 +22,15 @@ params {
     params.metapipeline_log_output_dir = "${params.output_dir}/log-test-call-sSV"
 
     params.sample_data = [
-        'GZLUCPTA000001-T001-P01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24143': [
+            'patient': 'IlluminaPatient1',
             'state': 'tumor',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0053040010_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24143/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24143.bam', 'contamination_table':'']
         ],
-        'GZLUCPTA000001-N001-B01-F': [
-            'patient': 'GZLUCPTA000001',
+        'NA24149': [
+            'patient': 'IlluminaPatient1',
             'state': 'normal',
-            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-gSNP/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_gSNP/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/CPT0040210002_realigned_recalibrated_reheadered.bam', 'contamination_table':'']
+            'recalibrate-BAM': ['BAM':'/hot/software/pipeline/metapipeline-DNA/Nextflow/development/input/data/BAM/NA24149/BWA-MEM2-2.2.1_GATK-4.2.4.1_IlluminaSampleTest_NA24149.bam', 'contamination_table':'']
         ]
     ]