Sfitz add intervals

CHANGELOG.md

@@ -10,6 +10,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [Unreleased]
 
 ### Added
+- Add `CollectHsMetrics`
+- Add `intervals_bed` option
 - Add `mosdepth` quantize workflow
 - Add `mosdepth` coverage windows workflow
 - Add `FastQC` workflow

config/F16.config

@@ -35,7 +35,7 @@ process {
     }
     withName: assess_coverage_mosdepth {
         cpus = 1
-        memory = 3.GB
+        memory = 8.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -93,6 +93,20 @@ process {
             }
         }
     }
+    withName: run_BedToIntervalList_picard {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_CollectHsMetrics_Picard {
+        cpus = 1
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 1.GB
+            }
+        }
+    }
     withName: run_bamqc_Qualimap {
         cpus = 4
         memory = 24.GB

config/F2.config

@@ -35,7 +35,7 @@ process {
     }
     withName: assess_coverage_mosdepth {
         cpus = 1
-        memory = 1.5.GB
+        memory = 4.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -103,6 +103,20 @@ process {
             }
         }
     }
+    withName: run_BedToIntervalList_picard {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_CollectHsMetrics_Picard {
+        cpus = 1
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 1.GB
+            }
+        }
+    }
     withName: run_bamqc_Qualimap {
         cpus = 2
         memory = 4.GB

config/F32.config

@@ -35,7 +35,7 @@ process {
     }
     withName: assess_coverage_mosdepth {
         cpus = 1
-        memory = 3.GB
+        memory = 8.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -93,6 +93,20 @@ process {
             }
         }
     }
+    withName: run_BedToIntervalList_picard {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_CollectHsMetrics_Picard {
+        cpus = 1
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 1.GB
+            }
+        }
+    }
     withName: run_bamqc_Qualimap {
         cpus = 4
         memory = 46.GB

config/F4.config

@@ -34,8 +34,8 @@ process {
         }
     }
     withName: assess_coverage_mosdepth {
-        cpus = 2
-        memory = 2.GB
+        cpus = 1
+        memory = 7.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -93,6 +93,21 @@ process {
             }
         }
     }
+    withName: run_BedToIntervalList_picard {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_CollectHsMetrics_Picard {
+        cpus = 1
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 1.GB
+            }
+        }
+    }
+
     withName: run_bamqc_Qualimap {
         cpus = 2
         memory = 4.GB

config/F72.config

@@ -35,7 +35,7 @@ process {
     }
     withName: assess_coverage_mosdepth {
         cpus = 1
-        memory = 3.GB
+        memory = 8.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -93,6 +93,20 @@ process {
             }
         }
     }
+    withName: run_BedToIntervalList_picard {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_CollectHsMetrics_Picard {
+        cpus = 1
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 1.GB
+            }
+        }
+    }
     withName: run_bamqc_Qualimap {
         cpus = 4
         memory = 56.GB

config/F8.config

@@ -35,7 +35,7 @@ process {
     }
     withName: assess_coverage_mosdepth {
         cpus = 1
-        memory = 2.GB
+        memory = 8.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -93,6 +93,20 @@ process {
             }
         }
     }
+    withName: run_BedToIntervalList_picard {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_CollectHsMetrics_Picard {
+        cpus = 1
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 1.GB
+            }
+        }
+    }
     withName: run_bamqc_Qualimap {
         cpus = 4
         memory = 9.GB

config/M64.config

@@ -35,7 +35,7 @@ process {
     }
     withName: assess_coverage_mosdepth {
         cpus = 1
-        memory = 3.GB
+        memory = 8.GB
         retry_strategy {
             memory {
                 strategy = 'add'
@@ -93,6 +93,20 @@ process {
             }
         }
     }
+    withName: run_BedToIntervalList_picard {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_CollectHsMetrics_Picard {
+        cpus = 1
+        memory = 1.GB
+        retry_strategy {
+            memory {
+                strategy = 'add'
+                operand = 1.GB
+            }
+        }
+    }
     withName: run_bamqc_Qualimap {
         cpus = 16
         memory = 38.GB

config/custom_schema_types.config

@@ -29,9 +29,6 @@ custom_schema_types {
         }
     }
 
-    /**
-    *   Check list of resource updates
-    */
     check_resource_update_list = { Map options, String name, Map properties ->
         custom_schema_types.check_if_list(options[name], name)
         for (item in options[name]) {

config/schema.yaml

@@ -17,6 +17,7 @@ algorithm:
     - mosdepth_quantize
     - samtools_stats
     - collectwgsmetrics
+    - collecthsmetrics
     - qualimap_bamqc
   default:
     - samtools_stats
@@ -41,6 +42,11 @@ save_intermediate_files:
   required: false
   default: false
   help: 'The option to save the intermediate files'
+intervals_bed:
+  type: 'Path'
+  mode: 'r'
+  required: false
+  help: 'Absolute path to BED file with intervals to process'
 fastqc_level:
   type: 'String'
   required: true
@@ -78,6 +84,11 @@ stats_additional_options:
   allow_empty: true
   default: ''
   help: 'Additional arguments for SAMtools stats command'
+mosdepth_windows:
+  type: 'Integer'
+  required: false
+  default: 500
+  help: 'Window size (integer). Only used if intervals file is not provided'
 mosdepth_use_fast_algorithm:
   type: 'Bool'
   required: false
@@ -88,11 +99,6 @@ mosdepth_per_base_output:
   required: false
   default: true
   help: 'Output per-base coverage'
-mosdepth_window_size:
-  type: 'Integer'
-  required: false
-  default: 500
-  help: 'Window size for mosdepth coverage calculation'
 mosdepth_additional_options:
   type: 'String'
   required: false

config/template.config

@@ -8,22 +8,22 @@ includeConfig "${projectDir}/nextflow.config"
 
 // Inputs/parameters of the pipeline
 params {
-    algorithm = ['samtools_stats', 'collectwgsmetrics'] // 'fastqc', 'samtools_stats', 'collectwgsmetrics', 'mosdepth_quantize', 'mosdepth_coverage', 'qualimap_bamqc'
+    algorithm = ['samtools_stats', 'collectwgsmetrics'] // 'fastqc', 'samtools_stats', 'collectwgsmetrics', 'collecthsmetrics', 'mosdepth_quantize', 'mosdepth_coverage', 'qualimap_bamqc'
     reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
     output_dir = '/path/to/output/directory'
     blcds_registered_dataset = false // if you want the output to be registered
     save_intermediate_files = true
+    intervals_bed = ''
 
     // SAMtools stats options
     stats_max_rgs_per_sample = 20
     stats_remove_duplicates = false
     stats_additional_options = ''
 
-    // mosdepth window-base coverage options
-    // fast algorithm ignores read pair overlaps and should not be used on libraries with small insert sizes
-    mosdepth_use_fast_algorithm = false
+    // mosdepth window-based coverage options
+    mosdepth_windows = 500  // not used if intervals_bed is defined
+    mosdepth_use_fast_algorithm = false // fast algorithm ignores read pair overlaps and should not be used on libraries with small insert sizes
     mosdepth_per_base_output = true
-    mosdepth_window_size = 500
     mosdepth_additional_options = '--mapq 20'
 
     // mosdepth quantized coverage (like GATK's Callable Regions)
@@ -36,14 +36,22 @@ params {
     mosdepth_quantize_additional_options = '--mapq 20'
 
     // Picard CollectWgsMetrics options
-    cwm_coverage_cap = 1000
+    cwm_coverage_cap = 250
     cwm_minimum_mapping_quality = 20
     cwm_minimum_base_quality = 20
     cwm_use_fast_algorithm = false
     cwm_additional_options = ''
 
+    // Picard CollectHsMetrics options
+    chm_bait_intervals_bed = '' // if not defined, intevals_bed will be used
+    chm_coverage_cap = 2000
+    chm_minimum_mapping_quality = 20
+    chm_minimum_base_quality = 20
+    chm_per_base_output = true
+    chm_additional_options = ''
+
     // Qualimap bamqc options
-    bamqc_output_format = 'pdf' // 'html' or 'pdf'
+    bamqc_output_format = 'html' // 'html' or 'pdf'. html is needed to use with multiqc
     bamqc_additional_options = ''
 
     // FastQC options