add mapdamage downsampling

Author: TCLamnidis

conf/test_humanpopgen.config

@@ -24,47 +24,48 @@ process {
 }
 
 params {
-    config_profile_name                = 'Test human popgen profile'
-    config_profile_description         = 'Minimal test dataset to check pipeline function'
+    config_profile_name                    = 'Test human popgen profile'
+    config_profile_description             = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input                              = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv'
+    input                                  = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv'
 
     // Genome references
-    fasta                              = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz'
+    fasta                                  = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz'
 
     // Mapping
-    mapping_tool                       = 'bowtie2'
-    convert_inputbam                   = true
+    mapping_tool                           = 'bowtie2'
+    convert_inputbam                       = true
 
     // BAM filtering
-    run_bamfiltering                   = true
-    bamfiltering_minreadlength         = 30
-    bamfiltering_mappingquality        = 37
+    run_bamfiltering                       = true
+    bamfiltering_minreadlength             = 30
+    bamfiltering_mappingquality            = 37
 
     // Damage
-    damagecalculation_tool             = 'mapdamage'
-    run_trim_bam                       = true
+    damagecalculation_tool                 = 'mapdamage'
+    damagecalculation_mapdamage_downsample = 10000
+    run_trim_bam                           = true
 
     // Contamination
-    run_mtnucratio                     = true
-    run_contamination_estimation_angsd = true
+    run_mtnucratio                         = true
+    run_contamination_estimation_angsd     = true
 
     // Genotyping
-    genotyping_tool                    = 'pileupcaller'
-    run_genotyping                     = true
-    genotyping_source                  = 'trimmed'
-    genotyping_pileupcaller_bedfile    = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
-    genotyping_pileupcaller_snpfile    = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K_covered_in_JK2067_downsampled_s0.1.numeric_chromosomes.snp'
+    genotyping_tool                        = 'pileupcaller'
+    run_genotyping                         = true
+    genotyping_source                      = 'trimmed'
+    genotyping_pileupcaller_bedfile        = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
+    genotyping_pileupcaller_snpfile        = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K_covered_in_JK2067_downsampled_s0.1.numeric_chromosomes.snp'
 
     //Sex Determination
-    run_sexdeterrmine                  = true
-    sexdeterrmine_bedfile              = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
+    run_sexdeterrmine                      = true
+    sexdeterrmine_bedfile                  = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
 
     // Metagenomics
-    run_metagenomics                   = true
-    metagenomics_complexity_tool       = 'prinseq'
-    metagenomics_profiling_tool        = 'kraken2'
-    metagenomics_profiling_database    = params.pipelines_testdata_base_path + 'eager/databases/kraken/eager_test.tar.gz'
-    metagenomics_run_postprocessing    = true
+    run_metagenomics                       = true
+    metagenomics_complexity_tool           = 'prinseq'
+    metagenomics_profiling_tool            = 'kraken2'
+    metagenomics_profiling_database        = params.pipelines_testdata_base_path + 'eager/databases/kraken/eager_test.tar.gz'
+    metagenomics_run_postprocessing        = true
 }