From a114f3c2a45cc038a08fba605f83be8e3b792557 Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Wed, 20 Mar 2024 13:58:36 -0700
Subject: [PATCH 01/12] use function to generate filenames

---
 module/depth_to_bed.nf             | 13 +++++++++-
 module/filter_off_target_depth.nf  | 38 ++++++++++++++++++++++++++----
 module/get_depth_samtools.nf       | 11 ++++++++-
 module/merge_bedfiles_bedtools.nf  | 13 +++++++++-
 module/merge_intervals_bedtools.nf | 13 +++++++++-
 module/run_HS_metrics.nf           | 25 ++++++++++++++++++--
 6 files changed, 103 insertions(+), 10 deletions(-)

diff --git a/module/depth_to_bed.nf b/module/depth_to_bed.nf
index 31f30ea..44f41fe 100644
--- a/module/depth_to_bed.nf
+++ b/module/depth_to_bed.nf
@@ -1,3 +1,4 @@
+include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
 /*
 *   Module/process description here
 *
@@ -32,12 +33,22 @@ process convert_depth_to_bed {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "SAMtools-${params.samtools_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "${tag}-depth-per-base.bed"
+        ]
+    )
+
     """
     set -euo pipefail
 
     cat ${input_tsv} | \
     awk 'BEGIN {OFS="\t"} {chr = \$1; start=\$2-1; stop=\$2; depth=\$3; print chr,start,stop,depth}' \
         | sort -k1,1 -k2,2n \
-        > ${params.sample_id}.${tag}_depth-per-base.bed
+        > ${output_filename}
     """
 }
diff --git a/module/filter_off_target_depth.nf b/module/filter_off_target_depth.nf
index 9c648bf..7d44a7a 100644
--- a/module/filter_off_target_depth.nf
+++ b/module/filter_off_target_depth.nf
@@ -1,4 +1,4 @@
-
+include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
 /*
 *   Filter for sites with read depth above a minimum threshold.
 *   Important for excluding near-target regions from off-target calculations.
@@ -28,6 +28,16 @@ process run_depth_filter {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "SAMtools-${params.samtools_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "depth-filtered.bed"
+        ]
+    )
+
     """
     set -euo pipefail
 
@@ -35,7 +45,7 @@ process run_depth_filter {
         -v min_depth="${params.min_read_depth}" \
         '\$4 >= min_depth' \
         ${input} \
-        > ${params.sample_id}.depth-filtered.bed
+        > ${output_filename}
         """
 }
 
@@ -73,6 +83,16 @@ process run_slop_BEDtools {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "BEDtools-${params.bedtools_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "${tag}_slop-${slop}.bed"
+        ]
+    )
+
     """
     set -euo pipefail
 
@@ -81,7 +101,7 @@ process run_slop_BEDtools {
         -i ${target_bed} \
         -g ${genome_sizes} \
         -b ${slop} \
-        > ${params.sample_id}.${tag}_slop-${slop}.bed
+        > ${output_filename}
     """
 }
 
@@ -113,6 +133,16 @@ process run_intersect_BEDtools {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "BEDtools-${params.bedtools_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "off-target-dbSNP_depth-per-base.bed"
+        ]
+    )
+
     """
     set -euo pipefail
 
@@ -121,6 +151,6 @@ process run_intersect_BEDtools {
         -a ${off_target_bed} \
         -b ${target_bed} \
         -v \
-        > ${params.sample_id}.off-target-dbSNP_depth-per-base.bed
+        > ${output_filename}
     """
 }
diff --git a/module/get_depth_samtools.nf b/module/get_depth_samtools.nf
index dc285a4..175eb10 100644
--- a/module/get_depth_samtools.nf
+++ b/module/get_depth_samtools.nf
@@ -1,3 +1,4 @@
+include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
 /*
 *   Module/process description here
 *
@@ -28,6 +29,14 @@ process run_depth_SAMtools {
         path ".command.*"
 
     script:
+    output_filename = generate_standard_filename(
+        "SAMtools-${params.samtools_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "${tag}-depth-per-base.tsv"
+        ]
+    )
     """
     set -euo pipefail
 
@@ -38,7 +47,7 @@ process run_depth_SAMtools {
         -aa \
         --min-BQ ${params.min_base_quality} \
         --min-MQ ${params.min_mapping_quality} \
-        -o ${params.sample_id}.${tag}.depth_per_base.tsv \
+        -o ${output_filename} \
         ${params.samtools_depth_extra_args}
     """
 }
diff --git a/module/merge_bedfiles_bedtools.nf b/module/merge_bedfiles_bedtools.nf
index 5a6bfe4..5818b0f 100644
--- a/module/merge_bedfiles_bedtools.nf
+++ b/module/merge_bedfiles_bedtools.nf
@@ -1,3 +1,4 @@
+include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
 /*
 *   Module/process description here
 *
@@ -26,6 +27,16 @@ process merge_bedfiles_BEDtools {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "BEDtools-${params.bedtools_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "target-with-enriched-off-target-intervals.bed"
+        ]
+    )
+
     """
     set -euo pipefail
 
@@ -33,6 +44,6 @@ process merge_bedfiles_BEDtools {
         sort -k1,1 -k2,2n | \
         awk '{OFS = "\t"}{print \$1, \$2, \$3}' | \
         bedtools merge \
-        > ${params.sample_id}.target_with_enriched_off-target_intervals.bed
+        > ${output_filename}
     """
 }
diff --git a/module/merge_intervals_bedtools.nf b/module/merge_intervals_bedtools.nf
index 6919bef..d48d883 100644
--- a/module/merge_intervals_bedtools.nf
+++ b/module/merge_intervals_bedtools.nf
@@ -1,3 +1,4 @@
+include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
 /*
 *   Module/process description here
 *
@@ -25,6 +26,16 @@ process run_merge_BEDtools {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "BEDtools-${params.bedtools_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "collapsed-coverage.bed"
+        ]
+    )
+
     """
     set -euo pipefail
 
@@ -33,6 +44,6 @@ process run_merge_BEDtools {
         -i ${input_depth_bed} \
         -c 4 \
         -o ${params.merge_operation} \
-        > ${params.sample_id}.collapsed_coverage.bed
+        > ${output_filename}
     """
 }
diff --git a/module/run_HS_metrics.nf b/module/run_HS_metrics.nf
index 72541d7..7fddf41 100644
--- a/module/run_HS_metrics.nf
+++ b/module/run_HS_metrics.nf
@@ -1,3 +1,4 @@
+include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
 /*
 *   Module/process description here
 *
@@ -34,6 +35,16 @@ process run_BedToIntervalList_picard {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "Picard-${params.picard_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': "${tag}.interval_list"
+        ]
+    )
+
     """
     set -euo pipefail
 
@@ -41,7 +52,7 @@ process run_BedToIntervalList_picard {
     -jar /usr/local/share/picard-slim-${params.picard_version}-0/picard.jar \
         BedToIntervalList \
         --INPUT $input_bed \
-        --OUTPUT ${params.sample_id}.${tag}.interval_list \
+        --OUTPUT ${output_filename} \
         --SEQUENCE_DICTIONARY $reference_dict \
         --SORT false
     """
@@ -70,6 +81,16 @@ process run_CollectHsMetrics_picard {
         path ".command.*"
 
     script:
+
+    output_filename = generate_standard_filename(
+        "Picard-${params.picard_version}",
+        params.dataset_id,
+        params.sample_id,
+        [
+            'additional_information': ["${tag}.HsMetrics.txt"]
+        ]
+    )
+
     """
     set -euo pipefail
 
@@ -79,7 +100,7 @@ process run_CollectHsMetrics_picard {
         --BAIT_INTERVALS $bait_interval_list \
         --INPUT $input_bam \
         --TARGET_INTERVALS $target_interval_list \
-        --OUTPUT ${params.sample_id}.HsMetrics.txt \
+        --OUTPUT ${output_filename} \
         --COVERAGE_CAP ${params.coverage_cap} \
         ${params.picard_CollectHsMetrics_extra_args} \
         --NEAR_DISTANCE ${params.near_distance} \

From 847aa17703914f40b7601e4f144e734c91068057 Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Wed, 20 Mar 2024 14:10:24 -0700
Subject: [PATCH 02/12] update test cases

---
 nftest.yml               | 12 ++++++------
 test/configtest-F16.json |  2 +-
 test/nftest.config       |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/nftest.yml b/nftest.yml
index e391b7c..80748c1 100644
--- a/nftest.yml
+++ b/nftest.yml
@@ -12,21 +12,21 @@ cases:
     skip: false
     verbose: true
     asserts:
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed
+      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed.sha512
+      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage.bed.sha512
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed.sha512
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed
+      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_off-target-dbSNP-depth-per-base.bed
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed.sha512
+      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_off-target-dbSNP-depth-per-base.bed.sha512
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed.sha512
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed
+      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_target-with-enriched-off-target-intervals.bed
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed.sha512
+      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_target-with-enriched-off-target-intervals.bed.sha512
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed.sha512
         method: md5
diff --git a/test/configtest-F16.json b/test/configtest-F16.json
index 6078e46..c5dff61 100644
--- a/test/configtest-F16.json
+++ b/test/configtest-F16.json
@@ -43,7 +43,7 @@
         "blcds_registered_dataset": false,
         "collect_metrics": true,
         "coverage_cap": "3000",
-        "dataset_id": "TWGSAMIN000001-T002-S02-F",
+        "dataset_id": "TWGSAMIN000001",
         "dataset_registry_prefix": "/hot/data",
         "date": "19970704T165655Z",
         "dbSNP_slop": "150",
diff --git a/test/nftest.config b/test/nftest.config
index 15d79ab..6ce26ac 100644
--- a/test/nftest.config
+++ b/test/nftest.config
@@ -9,7 +9,7 @@ includeConfig "${projectDir}/nextflow.config"
 // Inputs/parameters of the pipeline
 params {
     // sample inputs
-    dataset_id = 'TWGSAMIN000001-T002-S02-F'
+    dataset_id = 'TWGSAMIN000001'
     blcds_registered_dataset = false // if you want the output to be registered
 
     // reference files

From c654349b45d5c80e0d563cc103bffda0bc620b9f Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Wed, 20 Mar 2024 17:21:39 -0700
Subject: [PATCH 03/12] typo fixes

---
 module/run_HS_metrics.nf | 8 +++++---
 nftest.yml               | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/module/run_HS_metrics.nf b/module/run_HS_metrics.nf
index 7fddf41..251fde3 100644
--- a/module/run_HS_metrics.nf
+++ b/module/run_HS_metrics.nf
@@ -36,15 +36,17 @@ process run_BedToIntervalList_picard {
 
     script:
 
-    output_filename = generate_standard_filename(
+    output_filename_base = generate_standard_filename(
         "Picard-${params.picard_version}",
         params.dataset_id,
         params.sample_id,
         [
-            'additional_information': "${tag}.interval_list"
+            'additional_information': "${tag}"
         ]
     )
 
+    output_filename = "${output_filename_base}.interval_list"
+
     """
     set -euo pipefail
 
@@ -87,7 +89,7 @@ process run_CollectHsMetrics_picard {
         params.dataset_id,
         params.sample_id,
         [
-            'additional_information': ["${tag}.HsMetrics.txt"]
+            'additional_information': ".HsMetrics.txt"
         ]
     )
 
diff --git a/nftest.yml b/nftest.yml
index 80748c1..a60fabc 100644
--- a/nftest.yml
+++ b/nftest.yml
@@ -12,7 +12,7 @@ cases:
     skip: false
     verbose: true
     asserts:
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage
+      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage.bed
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed
         method: md5
       - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage.bed.sha512

From 8f08318a52d9d56adfc21898057ed4f34973df1b Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Thu, 21 Mar 2024 13:50:12 -0700
Subject: [PATCH 04/12] update HsMetrics extension

---
 module/run_HS_metrics.nf | 2 +-
 nftest.yml               | 9 ---------
 2 files changed, 1 insertion(+), 10 deletions(-)

diff --git a/module/run_HS_metrics.nf b/module/run_HS_metrics.nf
index 251fde3..ef8e060 100644
--- a/module/run_HS_metrics.nf
+++ b/module/run_HS_metrics.nf
@@ -89,7 +89,7 @@ process run_CollectHsMetrics_picard {
         params.dataset_id,
         params.sample_id,
         [
-            'additional_information': ".HsMetrics.txt"
+            'additional_information': "HsMetrics.txt"
         ]
     )
 
diff --git a/nftest.yml b/nftest.yml
index a60fabc..656373d 100644
--- a/nftest.yml
+++ b/nftest.yml
@@ -15,18 +15,9 @@ cases:
       - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage.bed
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage.bed.sha512
-        expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed.sha512
-        method: md5
       - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_off-target-dbSNP-depth-per-base.bed
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_off-target-dbSNP-depth-per-base.bed.sha512
-        expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed.sha512
-        method: md5
       - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_target-with-enriched-off-target-intervals.bed
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_target-with-enriched-off-target-intervals.bed.sha512
-        expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed.sha512
-        method: md5

From ba73a5c2a76b8a3f920ed4d54bf427a2a82ee224 Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Thu, 21 Mar 2024 18:49:24 -0700
Subject: [PATCH 05/12] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index efe1e44..1db4751 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Changed
 - Update CI/CD workflow to use current image
 - Update samtools depth default output options
+- Update filenames to standardized format
 
 ## [v1.0.0-rc.2] - 2024-02-14
 ### Changed

From 08a9d29e84b91af710ed0c49008715a2ef462124 Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Thu, 21 Mar 2024 18:57:27 -0700
Subject: [PATCH 06/12] update readme

---
 README.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index ca4af5c..94adce3 100644
--- a/README.md
+++ b/README.md
@@ -119,12 +119,12 @@ A directed acyclic graph of your pipeline.
  Output and Output Parameter/Flag | Description |
 | ------------ | ------------------------ |
 | `output_dir` | Location where generated output should be saved. |
-| `.target-with-enriched-off-target-intervals.bed` | New target file including original target intervals and intervals encompassing coverage-enriched off-target dbSNP sites. |
-|`.off-target-dbSNP_depth-per-base.bed`|Per-base read depth at dbSNP loci outside of targeted regions.|
-| `.collapsed_coverage.bed` | Per-base read depth at specified target intervals, collapsed by interval. (OPTIONAL) Set `target_depth` in config file. |
-|`.target-depth-per-base.bed`|Per-base read depth at target intervals (not collapsed). (OPTIONAL) set `save_raw_target_bed` in config file.|
-|`.genome-wide-dbSNP_depth-per-base.bed`| Per-base read depth at all dbSNP loci. (OPTIONAL) Set `save_all_dbSNP` in config file.|
-| `.HsMetrics.txt` | QC output from CollectHsMetrics()|
+| `*target-with-enriched-off-target-intervals.bed` | New target file including original target intervals and intervals encompassing coverage-enriched off-target dbSNP sites. |
+|`*off-target-dbSNP-depth-per-base.bed`|Per-base read depth at dbSNP loci outside of targeted regions.|
+| `*collapsed_coverage.bed` | Per-base read depth at specified target intervals, collapsed by interval. (OPTIONAL) Set `target_depth` in config file. |
+|`*target-depth-per-base.bed`|Per-base read depth at target intervals (not collapsed). (OPTIONAL) set `save_raw_target_bed` in config file.|
+|`*genome-wide-dbSNP-depth-per-base.bed`| Per-base read depth at all dbSNP loci. (OPTIONAL) Set `save_all_dbSNP` in config file.|
+| `*HsMetrics.txt` | QC output from CollectHsMetrics()|
 | `.tsv`,`.bed` | Intermediate outputs of unformatted and unmerged depth files. (OPTIONAL) Set `save_intermediate_files` in config file. |
 | `.interval_list` | Intermediate output of target bed file converted to picard's interval list format. (OPTIONAL)  Set `save_interval_list` in config file. |
 | `report.html`, `timeline.html` and `trace.txt` | A Nextflowreport, timeline and trace files |

From 6e046d811e40fb0c0c8bdb5dbed695e0ad212206 Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Thu, 21 Mar 2024 19:01:13 -0700
Subject: [PATCH 07/12] update diagram labels

---
 docs/calculate-targeted-coverage-flow.puml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/calculate-targeted-coverage-flow.puml b/docs/calculate-targeted-coverage-flow.puml
index bd1a8ab..fbe24e5 100644
--- a/docs/calculate-targeted-coverage-flow.puml
+++ b/docs/calculate-targeted-coverage-flow.puml
@@ -25,9 +25,9 @@ rectangle "Target-Focused Workflow" {
     rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
     rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
     ' output files
-    rectangle ".target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
+    rectangle "*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
     ' QC files
-    rectangle ".HSMetrics.txt" as HSMetrics <<QCFile>>
+    rectangle "*HSMetrics.txt" as HSMetrics <<QCFile>>
 }
 
 
@@ -50,8 +50,8 @@ rectangle "Off-Target Workflow" {
     rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>
 
     ' output files
-    rectangle ".target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
-    rectangle ".off-target-dbSNP_depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
+    rectangle "*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
+    rectangle "*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
 
     ' end node
     rectangle "recalibrate-BAM" as RecalBAM #White

From ebec90b658dedc2aa7cb7111f0a9dc87ab9e72d7 Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Thu, 21 Mar 2024 19:02:46 -0700
Subject: [PATCH 08/12] remove old drawio diagram

---
 ...ine-calculate-targeted-coverage.drawio.svg | 518 ------------------
 1 file changed, 518 deletions(-)
 delete mode 100644 pipeline-calculate-targeted-coverage.drawio.svg

diff --git a/pipeline-calculate-targeted-coverage.drawio.svg b/pipeline-calculate-targeted-coverage.drawio.svg
deleted file mode 100644
index fb93d48..0000000
--- a/pipeline-calculate-targeted-coverage.drawio.svg
+++ /dev/null
@@ -1,518 +0,0 @@
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-                                Inputs
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-                                Target File
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-                                Filter for off-target sites
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-                <text x="760" y="375" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    Filter for off...
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-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 178px; height: 1px; padding-top: 550px; margin-left: 721px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 15px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Off-target dbSNP read depth BED
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-                        </div>
-                    </div>
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-                <text x="810" y="555" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="15px" text-anchor="middle">
-                    Off-target dbSNP read de...
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-        <path d="M 606.47 454.7 L 570 400" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 609.38 459.07 L 602.58 455.19 L 606.47 454.7 L 608.41 451.3 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
-        <path d="M 732.85 454.3 L 760 400" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 730.5 459 L 730.5 451.17 L 732.85 454.3 L 736.76 454.3 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
-        <path d="M 610 460 L 573.98 505.03" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 570.7 509.13 L 572.34 501.47 L 573.98 505.03 L 577.8 505.85 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="610" y="430" width="120" height="60" fill="#4682b4" stroke="#0e8088" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 460px; margin-left: 611px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Convert to BED
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-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="670" y="465" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    Convert to BED
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-            </switch>
-        </g>
-        <rect x="80" y="250" width="120" height="60" fill="#4682b4" stroke="#0e8088" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 280px; margin-left: 81px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Calculate Per-base Read Depth
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="140" y="285" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    Calculate Per-...
-                </text>
-            </switch>
-        </g>
-        <path d="M 310 343.63 L 310 310.55" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 310 348.88 L 306.5 341.88 L 310 343.63 L 313.5 341.88 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <path d="M 376.37 380 L 390.11 380 L 390.11 200 L 440 200" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 371.12 380 L 378.12 376.5 L 376.37 380 L 378.12 383.5 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="250" y="350" width="120" height="60" fill="#4682b4" stroke="#0e8088" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 380px; margin-left: 251px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Calculate Coverage Metrics
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-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="310" y="385" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    Calculate Cove...
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-            </switch>
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-        <path d="M 140 463.63 L 140 410" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 140 468.88 L 136.5 461.88 L 140 463.63 L 143.5 461.88 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <path d="M 50 530 L 70 470 L 230 470 L 210 530 Z" fill="#d5e8d4" stroke="#82b366" stroke-miterlimit="10" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 178px; height: 1px; padding-top: 500px; margin-left: 51px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 15px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Target read depth BED
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="140" y="505" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="15px" text-anchor="middle">
-                    Target read depth BED
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-            </switch>
-        </g>
-        <path d="M 310 463.63 L 310 410" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 310 468.88 L 306.5 461.88 L 310 463.63 L 313.5 461.88 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <path d="M 220 530 L 240 470 L 400 470 L 380 530 Z" fill="#fff2cc" stroke="#d6b656" stroke-miterlimit="10" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 178px; height: 1px; padding-top: 500px; margin-left: 221px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 15px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                HS Metrics TXT
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="310" y="505" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="15px" text-anchor="middle">
-                    HS Metrics TXT
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-            </switch>
-        </g>
-        <path d="M 870.01 173.63 L 870.11 60 L 340.11 60 L 340 70" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 870 178.88 L 866.51 171.88 L 870.01 173.63 L 873.51 171.89 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="810" y="180" width="120" height="60" fill="#4682b4" stroke="#0e8088" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 210px; margin-left: 811px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Add Slop to Target Intervals
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="870" y="215" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    Add Slop to Ta...
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-            </switch>
-        </g>
-        <path d="M 140 343.63 L 140 310" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 140 348.88 L 136.5 341.88 L 140 343.63 L 143.5 341.88 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="80" y="350" width="120" height="60" fill="#4682b4" stroke="#0e8088" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 380px; margin-left: 81px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Convert to BED
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="140" y="385" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    Convert to BED
-                </text>
-            </switch>
-        </g>
-        <path d="M 450 773.63 L 450 746" fill="none" stroke="#000000" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 450 778.88 L 446.5 771.88 L 450 773.63 L 453.5 771.88 Z" fill="#000000" stroke="#000000" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="390" y="780" width="120" height="60" fill="rgb(255, 255, 255)" stroke="rgb(0, 0, 0)" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 810px; margin-left: 391px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                recalibrate-BAM
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="450" y="815" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    recalibrate-BAM
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-            </switch>
-        </g>
-        <path d="M 980 240.55 L 1000 180.55 L 1080 180.55 L 1060 240.55 Z" fill="#fff2cc" stroke="#d6b656" stroke-miterlimit="10" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 98px; height: 1px; padding-top: 211px; margin-left: 981px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 15px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                QC
-                                <br/>
-                                File
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="1030" y="215" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="15px" text-anchor="middle">
-                    QC...
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-            </switch>
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-        <path d="M 980 310.55 L 1000 250.55 L 1080 250.55 L 1060 310.55 Z" fill="#d5e8d4" stroke="#82b366" stroke-miterlimit="10" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 98px; height: 1px; padding-top: 281px; margin-left: 981px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 15px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Output
-                                <br/>
-                                File
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="1030" y="285" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="15px" text-anchor="middle">
-                    Output...
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-            </switch>
-        </g>
-        <path d="M 980 170.55 L 1000 110.55 L 1080 110.55 L 1060 170.55 Z" fill="#b46e46" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 98px; height: 1px; padding-top: 141px; margin-left: 981px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 15px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Input
-                                <br/>
-                                File
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="1030" y="145" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="15px" text-anchor="middle">
-                    Input...
-                </text>
-            </switch>
-        </g>
-        <path d="M 1083.63 360.55 L 970 360.55" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 1088.88 360.55 L 1081.88 364.05 L 1083.63 360.55 L 1081.88 357.05 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <path d="M 1083.63 398.33 L 970 398.33" fill="none" stroke="#000000" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 1088.88 398.33 L 1081.88 401.83 L 1083.63 398.33 L 1081.88 394.83 Z" fill="#000000" stroke="#000000" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="945" y="330" width="150" height="30" fill="none" stroke="none" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 1px; height: 1px; padding-top: 345px; margin-left: 1020px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: nowrap;">
-                                Target-focused workflow
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="1020" y="349" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">
-                    Target-focused workflow
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-            </switch>
-        </g>
-        <rect x="960" y="370" width="120" height="30" fill="none" stroke="none" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 1px; height: 1px; padding-top: 385px; margin-left: 1020px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 12px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: nowrap;">
-                                Off-target workflow
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-                        </div>
-                    </div>
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-                <text x="1020" y="389" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="12px" text-anchor="middle">
-                    Off-target workflow
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-            </switch>
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-        <path d="M 310.01 244.18 L 310.11 170 L 340.11 170 L 340 130" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 310 249.43 L 306.51 242.43 L 310.01 244.18 L 313.51 242.44 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <path d="M 243.63 280.59 L 230.11 280.67 L 230.11 130 L 180 130" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 248.88 280.56 L 241.9 284.1 L 243.63 280.59 L 241.86 277.1 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="250" y="250.55" width="120" height="60" fill="#4682b4" stroke="#0e8088" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 281px; margin-left: 251px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Convert BED to interval.list
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="310" y="286" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
-                    Convert BED to...
-                </text>
-            </switch>
-        </g>
-        <path d="M 256.37 100 L 270 100" fill="none" stroke="#0000ff" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 251.12 100 L 258.12 96.5 L 256.37 100 L 258.12 103.5 Z" fill="#0000ff" stroke="#0000ff" stroke-miterlimit="10" pointer-events="all"/>
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-        <g transform="translate(-0.5 -0.5)">
-            <switch>
-                <foreignObject pointer-events="none" width="100%" height="100%" requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility" style="overflow: visible; text-align: left;">
-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 158px; height: 1px; padding-top: 100px; margin-left: 101px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 15px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Bait File
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="180" y="105" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="15px" text-anchor="middle">
-                    Bait File
-                </text>
-            </switch>
-        </g>
-        <path d="M 510 540 L 450.11 540 L 450.01 583.63" fill="none" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="stroke"/>
-        <path d="M 450 588.88 L 446.52 581.87 L 450.01 583.63 L 453.52 581.89 Z" fill="rgb(0, 0, 0)" stroke="rgb(0, 0, 0)" stroke-miterlimit="10" pointer-events="all"/>
-        <rect x="510" y="510" width="120" height="60" fill="#4682b4" stroke="#0e8088" pointer-events="all"/>
-        <g transform="translate(-0.5 -0.5)">
-            <switch>
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-                    <div xmlns="http://www.w3.org/1999/xhtml" style="display: flex; align-items: unsafe center; justify-content: unsafe center; width: 118px; height: 1px; padding-top: 540px; margin-left: 511px;">
-                        <div data-drawio-colors="color: rgb(0, 0, 0); " style="box-sizing: border-box; font-size: 0px; text-align: center;">
-                            <div style="display: inline-block; font-size: 17px; font-family: Helvetica; color: rgb(0, 0, 0); line-height: 1.2; pointer-events: all; white-space: normal; overflow-wrap: normal;">
-                                Add Slop to off-target SNPs
-                            </div>
-                        </div>
-                    </div>
-                </foreignObject>
-                <text x="570" y="545" fill="rgb(0, 0, 0)" font-family="Helvetica" font-size="17px" text-anchor="middle">
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-            </switch>
-        </g>
-    </g>
-    <switch>
-        <g requiredFeatures="http://www.w3.org/TR/SVG11/feature#Extensibility"/>
-        <a transform="translate(0,-5)" xlink:href="https://www.diagrams.net/doc/faq/svg-export-text-problems" target="_blank">
-            <text text-anchor="middle" font-size="10px" x="50%" y="100%">
-                Text is not SVG - cannot display
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-        </a>
-    </switch>
-</svg>
\ No newline at end of file

From f20c65132f214d5a2e3d09c8bf4823cc27362168 Mon Sep 17 00:00:00 2001
From: alkaZeltser <alkaZeltser@users.noreply.github.com>
Date: Fri, 22 Mar 2024 02:03:23 +0000
Subject: [PATCH 09/12] Update SVG images for PlantUML diagrams

---
 docs/calculate-targeted-coverage-flow.svg | 94 +++++++++++------------
 1 file changed, 47 insertions(+), 47 deletions(-)

diff --git a/docs/calculate-targeted-coverage-flow.svg b/docs/calculate-targeted-coverage-flow.svg
index 6f6ed1e..17857ed 100644
--- a/docs/calculate-targeted-coverage-flow.svg
+++ b/docs/calculate-targeted-coverage-flow.svg
@@ -1,37 +1,37 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="892px" preserveAspectRatio="none" style="width:1353px;height:892px;background:#FFFFFF;" version="1.1" viewBox="0 0 1353 892" width="1353px" zoomAndPan="magnify"><defs/><g><!--MD5=[5793b8a6652117c897ab2de440c96a33]
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="892px" preserveAspectRatio="none" style="width:1359px;height:892px;background:#FFFFFF;" version="1.1" viewBox="0 0 1359 892" width="1359px" zoomAndPan="magnify"><defs/><g><!--MD5=[5793b8a6652117c897ab2de440c96a33]
 cluster Target-Focused Workflow--><g id="cluster_Target-Focused Workflow"><rect height="495" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="512" x="7" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="205" x="160.5" y="21.9951">Target-Focused Workflow</text></g><!--MD5=[d541b56f1a19ef419b51f0e2d36e069b]
 cluster Input1--><g id="cluster_Input1"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="233" x="77" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="193.5" y="52">Input</text></g><!--MD5=[fdf0c65af9cafec17be4ce373e959a1e]
-cluster Off-Target Workflow--><g id="cluster_Off-Target Workflow"><rect height="879" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="600" x="543" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="162" x="762" y="21.9951">Off-Target Workflow</text></g><!--MD5=[fcfe6af240cbb9de2e31d0010bc81b0a]
-cluster Input2--><g id="cluster_Input2"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="343" x="663" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="834.5" y="52">Input</text></g><!--MD5=[f7217341b3bb6bbf768c7f0e049f8d09]
-cluster Legend--><g id="cluster_Legend"><rect height="375" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="180" x="1167" y="31"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="59" x="1227.5" y="45.9951">Legend</text></g><!--MD5=[a83f4c4b109093b6df97f2e5475fbb6d]
+cluster Off-Target Workflow--><g id="cluster_Off-Target Workflow"><rect height="879" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="606" x="543" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="162" x="765" y="21.9951">Off-Target Workflow</text></g><!--MD5=[fcfe6af240cbb9de2e31d0010bc81b0a]
+cluster Input2--><g id="cluster_Input2"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="343" x="665" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="836.5" y="52">Input</text></g><!--MD5=[f7217341b3bb6bbf768c7f0e049f8d09]
+cluster Legend--><g id="cluster_Legend"><rect height="375" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="180" x="1173" y="31"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="59" x="1233.5" y="45.9951">Legend</text></g><!--MD5=[a83f4c4b109093b6df97f2e5475fbb6d]
 entity BAM1--><g id="elem_BAM1"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="355.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="365.5" y="88.9951">BAM</text></g><!--MD5=[afbb0db1cbcdc0e923b4432d737361e0]
 entity ValInputs1--><g id="elem_ValInputs1"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="320.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="330.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b3fc1d5769c32d62159879ccf9acacb3]
 entity CalcReadDepth--><g id="elem_CalcReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="237" x="265.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="217" x="275.5" y="280.9951">Calculate Per-Base Read Depth</text></g><!--MD5=[bd6c7db5d87a2d4a9d8c6ffd88a5bcea]
 entity ConvBEDtoIntervalList--><g id="elem_ConvBEDtoIntervalList"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="202" x="29" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="182" x="39" y="184.9951">Convert BED to interval.list</text></g><!--MD5=[2c5b443c033a35a14a0a2ae3c89dfd10]
 entity ConvtoBED1--><g id="elem_ConvtoBED1"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="321" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="331" y="376.9951">Convert to BED</text></g><!--MD5=[b356e89eaf00e777fdf024a4814b8e18]
 entity CalcCovMetrics--><g id="elem_CalcCovMetrics"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="207" x="23.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="187" x="33.5" y="280.9951">Calculate Coverage Metrics</text></g><!--MD5=[dcd1f042f3b348163f3493299ca35159]
-entity TargetReadDepthBED--><g id="elem_TargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="209" x="279.5" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="189" x="289.5" y="472.9951">.target-depth-per-base.bed</text></g><!--MD5=[360be6d182cb7145dcbdee0021c8ccd3]
-entity HSMetrics--><g id="elem_HSMetrics"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="114" x="70" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="94" x="80" y="376.9951">.HSMetrics.txt</text></g><!--MD5=[07ce715d8952035f1c648a97cce063ab]
+entity TargetReadDepthBED--><g id="elem_TargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="218" x="275" y="450"/><ellipse cx="290.5" cy="468.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="185" x="298" y="472.9951">target-depth-per-base.bed</text></g><!--MD5=[360be6d182cb7145dcbdee0021c8ccd3]
+entity HSMetrics--><g id="elem_HSMetrics"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="123" x="65.5" y="354"/><ellipse cx="81" cy="372.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="90" x="88.5" y="376.9951">HSMetrics.txt</text></g><!--MD5=[07ce715d8952035f1c648a97cce063ab]
 entity TargetFile1--><g id="elem_TargetFile1"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="202" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="212" y="88.9951">Target File</text></g><!--MD5=[bb2b4fcf43ed25e0ab855486922ad703]
 entity BaitFile--><g id="elem_BaitFile"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="73" x="93.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="53" x="103.5" y="88.9951">Bait File</text></g><!--MD5=[3711304ccc2c64bce48f9718f643142e]
-entity ValInputs2--><g id="elem_ValInputs2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="912.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="922.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b6607c3669bb86c4076734be7bd06d49]
-entity CalcReadDepthAtdbSNP--><g id="elem_CalcReadDepthAtdbSNP"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="272" x="842" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="252" x="852" y="280.9951">Cacluate Read Depth at dbSNP Sites</text></g><!--MD5=[5bda774f1e672053773e83dd05eacaed]
-entity FilterReadDepth--><g id="elem_FilterReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="228" x="882" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="208" x="892" y="472.9951">Filter for Minimum Read Depth</text></g><!--MD5=[cd6e518d9ba44279cfc888103d8aa6a4]
-entity FilterOffTarget--><g id="elem_FilterOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="186" x="645" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="166" x="655" y="472.9951">Filter for Off-Target Sites</text></g><!--MD5=[715b69296de685ae7f1f45cea8134010]
-entity ConvtoBED2--><g id="elem_ConvtoBED2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="915" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="925" y="376.9951">Convert to BED</text></g><!--MD5=[0c145ebd8b2b512a07df55d1a2465d38]
-entity AddSlopOffTarget--><g id="elem_AddSlopOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="212" x="915" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="192" x="925" y="568.9951">Add Slop to Off-Target SNPs</text></g><!--MD5=[f50d1513eea2cf224a813b3b0f46f551]
-entity MergeWithTarget--><g id="elem_MergeWithTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="172" x="757" y="642"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="152" x="767" y="664.9951">Merge with Target File</text></g><!--MD5=[6b0d55934776f8df877a4aa9a84c95b4]
-entity AddSlopTarget--><g id="elem_AddSlopTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="209" x="597.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="189" x="607.5" y="280.9951">Add Slop to Target Intervals</text></g><!--MD5=[97b99327512678a3edfd748478556652]
-entity TargetPlusOffTargetReadDepthBED--><g id="elem_TargetPlusOffTargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="325" x="680.5" y="738"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="305" x="690.5" y="760.9951">.target-with-enriched-off-target-intervals.bed</text></g><!--MD5=[7f5ec864b4cb369ae6c755b0ecd8ff52]
-entity OffTargetReadDepth--><g id="elem_OffTargetReadDepth"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="284" x="596" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="264" x="606" y="568.9951">.off-target-dbSNP_depth-per-base.bed</text></g><!--MD5=[e94e62f06dcbdb4a6e54560988436e02]
-entity RecalBAM--><g id="elem_RecalBAM"><rect fill="#FFFFFF" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="128" x="779" y="834"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="108" x="789" y="856.9951">recalibrate-BAM</text></g><!--MD5=[d240438f19e54a6f2cb3889e6527a070]
-entity TargetFile2--><g id="elem_TargetFile2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="679" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="689" y="88.9951">Target File</text></g><!--MD5=[7b92cfaf277f583add5cf6dde83011d4]
-entity dbSNP_VCF--><g id="elem_dbSNP_VCF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="97" x="806.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="77" x="816.5" y="88.9951">dbSNP VCF</text></g><!--MD5=[0b8015d1c6b7568455913bd022baae3a]
-entity BAM2--><g id="elem_BAM2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="938.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="948.5" y="88.9951">BAM</text></g><!--MD5=[486a548dd2b54905abbe5c1ab7fa9983]
-entity IF--><g id="elem_IF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="82" x="1216" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="62" x="1226" y="88.9951">Input File</text></g><!--MD5=[d3ef473a5067122b9254af2bc2f25065]
-entity QC--><g id="elem_QC"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="147" x="1183.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="127" x="1193.5" y="184.9951">Quality Control File</text></g><!--MD5=[633fdf3c843eeff0d0fbc3bde364bced]
-entity OF--><g id="elem_OF"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="95" x="1209.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="75" x="1219.5" y="280.9951">Output File</text></g><!--MD5=[7842cb4300efb401920d8f72ebe921e6]
-entity PS--><g id="elem_PS"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="112" x="1201" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="92" x="1211" y="376.9951">Process Step</text></g><!--MD5=[4ebbafa84b39c454a0f1728fb61efbcb]
+entity ValInputs2--><g id="elem_ValInputs2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="914.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="924.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b6607c3669bb86c4076734be7bd06d49]
+entity CalcReadDepthAtdbSNP--><g id="elem_CalcReadDepthAtdbSNP"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="272" x="844" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="252" x="854" y="280.9951">Cacluate Read Depth at dbSNP Sites</text></g><!--MD5=[5bda774f1e672053773e83dd05eacaed]
+entity FilterReadDepth--><g id="elem_FilterReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="228" x="887" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="208" x="897" y="472.9951">Filter for Minimum Read Depth</text></g><!--MD5=[cd6e518d9ba44279cfc888103d8aa6a4]
+entity FilterOffTarget--><g id="elem_FilterOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="186" x="648" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="166" x="658" y="472.9951">Filter for Off-Target Sites</text></g><!--MD5=[715b69296de685ae7f1f45cea8134010]
+entity ConvtoBED2--><g id="elem_ConvtoBED2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="917" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="927" y="376.9951">Convert to BED</text></g><!--MD5=[0c145ebd8b2b512a07df55d1a2465d38]
+entity AddSlopOffTarget--><g id="elem_AddSlopOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="212" x="921" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="192" x="931" y="568.9951">Add Slop to Off-Target SNPs</text></g><!--MD5=[f50d1513eea2cf224a813b3b0f46f551]
+entity MergeWithTarget--><g id="elem_MergeWithTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="172" x="760" y="642"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="152" x="770" y="664.9951">Merge with Target File</text></g><!--MD5=[6b0d55934776f8df877a4aa9a84c95b4]
+entity AddSlopTarget--><g id="elem_AddSlopTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="209" x="599.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="189" x="609.5" y="280.9951">Add Slop to Target Intervals</text></g><!--MD5=[97b99327512678a3edfd748478556652]
+entity TargetPlusOffTargetReadDepthBED--><g id="elem_TargetPlusOffTargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="334" x="679" y="738"/><ellipse cx="694.5" cy="756.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="301" x="702" y="760.9951">target-with-enriched-off-target-intervals.bed</text></g><!--MD5=[7f5ec864b4cb369ae6c755b0ecd8ff52]
+entity OffTargetReadDepth--><g id="elem_OffTargetReadDepth"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="291" x="595.5" y="546"/><ellipse cx="611" cy="564.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="258" x="618.5" y="568.9951">off-target-dbSNP-depth-per-base.bed</text></g><!--MD5=[e94e62f06dcbdb4a6e54560988436e02]
+entity RecalBAM--><g id="elem_RecalBAM"><rect fill="#FFFFFF" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="128" x="782" y="834"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="108" x="792" y="856.9951">recalibrate-BAM</text></g><!--MD5=[d240438f19e54a6f2cb3889e6527a070]
+entity TargetFile2--><g id="elem_TargetFile2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="681" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="691" y="88.9951">Target File</text></g><!--MD5=[7b92cfaf277f583add5cf6dde83011d4]
+entity dbSNP_VCF--><g id="elem_dbSNP_VCF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="97" x="808.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="77" x="818.5" y="88.9951">dbSNP VCF</text></g><!--MD5=[0b8015d1c6b7568455913bd022baae3a]
+entity BAM2--><g id="elem_BAM2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="940.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="950.5" y="88.9951">BAM</text></g><!--MD5=[486a548dd2b54905abbe5c1ab7fa9983]
+entity IF--><g id="elem_IF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="82" x="1222" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="62" x="1232" y="88.9951">Input File</text></g><!--MD5=[d3ef473a5067122b9254af2bc2f25065]
+entity QC--><g id="elem_QC"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="147" x="1189.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="127" x="1199.5" y="184.9951">Quality Control File</text></g><!--MD5=[633fdf3c843eeff0d0fbc3bde364bced]
+entity OF--><g id="elem_OF"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="95" x="1215.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="75" x="1225.5" y="280.9951">Output File</text></g><!--MD5=[7842cb4300efb401920d8f72ebe921e6]
+entity PS--><g id="elem_PS"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="112" x="1207" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="92" x="1217" y="376.9951">Process Step</text></g><!--MD5=[4ebbafa84b39c454a0f1728fb61efbcb]
 link BAM1 to ValInputs1--><g id="link_BAM1_ValInputs1"><path d="M381,102.24 C381,117.48 381,139.81 381,156.46 " fill="none" id="BAM1-to-ValInputs1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="381,161.87,385,152.87,381,156.87,377,152.87,381,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0b188298c9b1afe471d4865e17af690e]
 link BaitFile to ConvBEDtoIntervalList--><g id="link_BaitFile_ConvBEDtoIntervalList"><path d="M130,102.24 C130,117.48 130,139.81 130,156.46 " fill="none" id="BaitFile-to-ConvBEDtoIntervalList" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="130,161.87,134,152.87,130,156.87,126,152.87,130,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[a98f2fcb5fff3f38e9b30ea7ce7944cc]
 reverse link BaitFile to TargetFile1--><g id="link_BaitFile_TargetFile1"><path d="M172.05,84 C181.94,84 191.84,84 201.73,84 " fill="none" id="BaitFile-backto-TargetFile1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="166.88,84,175.8914,87.9743,171.88,83.9857,175.8685,79.9743,166.88,84" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[8613a7106181726335c268ad9afcbade]
@@ -43,23 +43,23 @@ link ValInputs1 to CalcCovMetrics--><g id="link_ValInputs1_CalcCovMetrics"><path
 link CalcCovMetrics to HSMetrics--><g id="link_CalcCovMetrics_HSMetrics"><path d="M127,294.24 C127,309.48 127,331.81 127,348.46 " fill="none" id="CalcCovMetrics-to-HSMetrics" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="127,353.87,131,344.87,127,348.87,123,344.87,127,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[01f923ac9ec9e6500d1bb9fa79e1697e]
 link CalcReadDepth to ConvtoBED1--><g id="link_CalcReadDepth_ConvtoBED1"><path d="M384,294.24 C384,309.48 384,331.81 384,348.46 " fill="none" id="CalcReadDepth-to-ConvtoBED1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="384,353.87,388,344.87,384,348.87,380,344.87,384,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[af6509568e048ae4cd4a149100a354eb]
 link ConvtoBED1 to TargetReadDepthBED--><g id="link_ConvtoBED1_TargetReadDepthBED"><path d="M384,390.24 C384,405.48 384,427.81 384,444.46 " fill="none" id="ConvtoBED1-to-TargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="384,449.87,388,440.87,384,444.87,380,440.87,384,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ad70a8f2d24c7fbe93a363248ba8fd89]
-link TargetFile2 to AddSlopTarget--><g id="link_TargetFile2_AddSlopTarget"><path d="M722.92,102.2 C718.74,136.67 709.36,214.23 704.71,252.61 " fill="none" id="TargetFile2-to-AddSlopTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="704.06,257.98,709.1096,249.5241,704.6591,253.016,701.1672,248.5656,704.06,257.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bb9b1f52b6b7f984ba4d3d204d33fcda]
-link TargetFile2 to MergeWithTarget--><g id="link_TargetFile2_MergeWithTarget"><path d="M693.96,102.09 C646.17,130.94 560,194.18 560,275 C560,275 560,275 560,469 C560,519.86 544.35,543.87 578,582 C621.15,630.91 693.36,649.57 751.5,656.33 " fill="none" id="TargetFile2-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="756.73,656.91,748.2174,651.9567,751.7595,656.3672,747.349,659.9094,756.73,656.91" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0f5f9f541059e0d392cad8edec1088b0]
-link dbSNP_VCF to CalcReadDepthAtdbSNP--><g id="link_dbSNP_VCF_CalcReadDepthAtdbSNP"><path d="M858.38,102.24 C863.52,125.46 874.88,167.39 895,198 C909.66,220.29 932.1,240.59 949.96,254.75 " fill="none" id="dbSNP_VCF-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="953.93,257.85,949.3077,249.1532,949.9925,254.7685,944.3772,255.4532,953.93,257.85" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1085dcdb1e044111634ab5f4c085fbb6]
-link BAM2 to ValInputs2--><g id="link_BAM2_ValInputs2"><path d="M965.65,102.24 C967.12,117.61 969.28,140.2 970.88,156.89 " fill="none" id="BAM2-to-ValInputs2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="971.36,161.87,974.4685,152.5246,970.8752,156.8936,966.5062,153.3003,971.36,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[26102ab38cefa976c6f11175f31d78b3]
-link ValInputs2 to CalcReadDepthAtdbSNP--><g id="link_ValInputs2_CalcReadDepthAtdbSNP"><path d="M973.92,198.24 C974.73,213.48 975.92,235.81 976.8,252.46 " fill="none" id="ValInputs2-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="977.09,257.87,980.5948,248.6659,976.8182,252.8774,972.6067,249.1008,977.09,257.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bc906825f7e1d5b70f40674632bccb60]
-link AddSlopTarget to FilterOffTarget--><g id="link_AddSlopTarget_FilterOffTarget"><path d="M705.26,294.2 C711.79,328.67 726.49,406.23 733.76,444.61 " fill="none" id="AddSlopTarget-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="734.78,449.98,737.0394,440.3938,733.8517,445.0669,729.1785,441.8792,734.78,449.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[e6ec3830f61b2fc00c1f964c6c082250]
-link CalcReadDepthAtdbSNP to ConvtoBED2--><g id="link_CalcReadDepthAtdbSNP_ConvtoBED2"><path d="M978,294.24 C978,309.48 978,331.81 978,348.46 " fill="none" id="CalcReadDepthAtdbSNP-to-ConvtoBED2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="978,353.87,982,344.87,978,348.87,974,344.87,978,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[312c39a7f5e428ae64e27424907166bd]
-link ConvtoBED2 to FilterOffTarget--><g id="link_ConvtoBED2_FilterOffTarget"><path d="M934.54,390.02 C892.7,406.41 829.56,431.14 786.2,448.12 " fill="none" id="ConvtoBED2-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="781.54,449.95,791.3793,450.384,786.1941,448.1226,788.4555,442.9374,781.54,449.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ea959455ce9951d3e4721f89ee60932b]
-link ConvtoBED2 to FilterReadDepth--><g id="link_ConvtoBED2_FilterReadDepth"><path d="M981.3,390.24 C984.24,405.61 988.57,428.2 991.77,444.89 " fill="none" id="ConvtoBED2-to-FilterReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="992.72,449.87,994.9525,440.2775,991.7779,444.9596,987.0958,441.7849,992.72,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0e0a99d1d7bc0797a534b161d1c3fca8]
-link FilterReadDepth to AddSlopOffTarget--><g id="link_FilterReadDepth_AddSlopOffTarget"><path d="M1000.59,486.24 C1004.67,501.61 1010.68,524.2 1015.12,540.89 " fill="none" id="FilterReadDepth-to-AddSlopOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="1016.44,545.87,1017.9896,536.1438,1015.1535,541.0384,1010.2589,538.2023,1016.44,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1fe930d4fe042d6de6dd8d043965d9f2]
-link FilterOffTarget to OffTargetReadDepth--><g id="link_FilterOffTarget_OffTargetReadDepth"><path d="M738,486.24 C738,501.48 738,523.81 738,540.46 " fill="none" id="FilterOffTarget-to-OffTargetReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="738,545.87,742,536.87,738,540.87,734,536.87,738,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[be633c3fef0ea7de7d91abfc3ce66e7d]
-link AddSlopOffTarget to MergeWithTarget--><g id="link_AddSlopOffTarget_MergeWithTarget"><path d="M988.77,582.02 C958.11,598.21 912.04,622.54 879.93,639.5 " fill="none" id="AddSlopOffTarget-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="875.29,641.95,885.1175,641.3019,879.7155,639.623,881.3944,634.221,875.29,641.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0fa50402f24eb397243c00d2dc3ff62f]
-link MergeWithTarget to TargetPlusOffTargetReadDepthBED--><g id="link_MergeWithTarget_TargetPlusOffTargetReadDepthBED"><path d="M843,678.24 C843,693.48 843,715.81 843,732.46 " fill="none" id="MergeWithTarget-to-TargetPlusOffTargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="843,737.87,847,728.87,843,732.87,839,728.87,843,737.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[4737fbc0abd4b31898a08a11d07ff5b8]
-link TargetPlusOffTargetReadDepthBED to RecalBAM--><g id="link_TargetPlusOffTargetReadDepthBED_RecalBAM"><path d="M843,774.24 C843,789.48 843,811.81 843,828.46 " fill="none" id="TargetPlusOffTargetReadDepthBED-to-RecalBAM" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="843,833.87,847,824.87,843,828.87,839,824.87,843,833.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1d4d0dbdd50de0a0980321eccab73fac]
+link TargetFile2 to AddSlopTarget--><g id="link_TargetFile2_AddSlopTarget"><path d="M724.92,102.2 C720.74,136.67 711.36,214.23 706.71,252.61 " fill="none" id="TargetFile2-to-AddSlopTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="706.06,257.98,711.1096,249.5241,706.6591,253.016,703.1672,248.5656,706.06,257.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bb9b1f52b6b7f984ba4d3d204d33fcda]
+link TargetFile2 to MergeWithTarget--><g id="link_TargetFile2_MergeWithTarget"><path d="M695.2,102.22 C646.74,131.05 560,193.97 560,275 C560,275 560,275 560,469 C560,519.86 544.3,543.92 578,582 C601.61,608.67 686.64,630.13 754.67,643.55 " fill="none" id="TargetFile2-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="759.95,644.58,751.8807,638.9332,755.0422,643.6241,750.3513,646.7856,759.95,644.58" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0f5f9f541059e0d392cad8edec1088b0]
+link dbSNP_VCF to CalcReadDepthAtdbSNP--><g id="link_dbSNP_VCF_CalcReadDepthAtdbSNP"><path d="M860.38,102.24 C865.52,125.46 876.88,167.39 897,198 C911.66,220.29 934.1,240.59 951.96,254.75 " fill="none" id="dbSNP_VCF-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="955.93,257.85,951.3077,249.1532,951.9925,254.7685,946.3772,255.4532,955.93,257.85" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1085dcdb1e044111634ab5f4c085fbb6]
+link BAM2 to ValInputs2--><g id="link_BAM2_ValInputs2"><path d="M967.65,102.24 C969.12,117.61 971.28,140.2 972.88,156.89 " fill="none" id="BAM2-to-ValInputs2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="973.36,161.87,976.4685,152.5246,972.8752,156.8936,968.5062,153.3003,973.36,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[26102ab38cefa976c6f11175f31d78b3]
+link ValInputs2 to CalcReadDepthAtdbSNP--><g id="link_ValInputs2_CalcReadDepthAtdbSNP"><path d="M975.92,198.24 C976.73,213.48 977.92,235.81 978.8,252.46 " fill="none" id="ValInputs2-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="979.09,257.87,982.5948,248.6659,978.8182,252.8774,974.6067,249.1008,979.09,257.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bc906825f7e1d5b70f40674632bccb60]
+link AddSlopTarget to FilterOffTarget--><g id="link_AddSlopTarget_FilterOffTarget"><path d="M707.35,294.2 C714.06,328.67 729.17,406.23 736.64,444.61 " fill="none" id="AddSlopTarget-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="737.69,449.98,739.8956,440.3813,736.7341,445.0722,732.0432,441.9107,737.69,449.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[e6ec3830f61b2fc00c1f964c6c082250]
+link CalcReadDepthAtdbSNP to ConvtoBED2--><g id="link_CalcReadDepthAtdbSNP_ConvtoBED2"><path d="M980,294.24 C980,309.48 980,331.81 980,348.46 " fill="none" id="CalcReadDepthAtdbSNP-to-ConvtoBED2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="980,353.87,984,344.87,980,348.87,976,344.87,980,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[312c39a7f5e428ae64e27424907166bd]
+link ConvtoBED2 to FilterOffTarget--><g id="link_ConvtoBED2_FilterOffTarget"><path d="M936.72,390.02 C895.14,406.38 832.44,431.04 789.26,448.02 " fill="none" id="ConvtoBED2-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="784.36,449.95,794.2008,450.3475,789.0073,448.1054,791.2494,442.9118,784.36,449.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ea959455ce9951d3e4721f89ee60932b]
+link ConvtoBED2 to FilterReadDepth--><g id="link_ConvtoBED2_FilterReadDepth"><path d="M983.85,390.24 C987.29,405.61 992.33,428.2 996.06,444.89 " fill="none" id="ConvtoBED2-to-FilterReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="997.17,449.87,999.1224,440.2166,996.0853,444.9891,991.3129,441.952,997.17,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0e0a99d1d7bc0797a534b161d1c3fca8]
+link FilterReadDepth to AddSlopOffTarget--><g id="link_FilterReadDepth_AddSlopOffTarget"><path d="M1005.77,486.24 C1010.02,501.61 1016.27,524.2 1020.88,540.89 " fill="none" id="FilterReadDepth-to-AddSlopOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="1022.26,545.87,1023.7023,536.1273,1020.9203,541.0528,1015.9948,538.2708,1022.26,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1fe930d4fe042d6de6dd8d043965d9f2]
+link FilterOffTarget to OffTargetReadDepth--><g id="link_FilterOffTarget_OffTargetReadDepth"><path d="M741,486.24 C741,501.48 741,523.81 741,540.46 " fill="none" id="FilterOffTarget-to-OffTargetReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="741,545.87,745,536.87,741,540.87,737,536.87,741,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[be633c3fef0ea7de7d91abfc3ce66e7d]
+link AddSlopOffTarget to MergeWithTarget--><g id="link_AddSlopOffTarget_MergeWithTarget"><path d="M994.22,582.02 C963.05,598.21 916.21,622.54 883.55,639.5 " fill="none" id="AddSlopOffTarget-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="878.84,641.95,888.6707,641.3517,883.2773,639.6455,884.9835,634.2521,878.84,641.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0fa50402f24eb397243c00d2dc3ff62f]
+link MergeWithTarget to TargetPlusOffTargetReadDepthBED--><g id="link_MergeWithTarget_TargetPlusOffTargetReadDepthBED"><path d="M846,678.24 C846,693.48 846,715.81 846,732.46 " fill="none" id="MergeWithTarget-to-TargetPlusOffTargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="846,737.87,850,728.87,846,732.87,842,728.87,846,737.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[4737fbc0abd4b31898a08a11d07ff5b8]
+link TargetPlusOffTargetReadDepthBED to RecalBAM--><g id="link_TargetPlusOffTargetReadDepthBED_RecalBAM"><path d="M846,774.24 C846,789.48 846,811.81 846,828.46 " fill="none" id="TargetPlusOffTargetReadDepthBED-to-RecalBAM" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="846,833.87,850,824.87,846,828.87,842,824.87,846,833.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1d4d0dbdd50de0a0980321eccab73fac]
 link IF to QC--><!--MD5=[03c241bed99ac1776e7d8c4bd4f5cca5]
 link QC to OF--><!--MD5=[35700df3515afd241139af4c0386ffe2]
-link OF to PS--><!--MD5=[92f34df3065afc79e8f831e044f7297a]
+link OF to PS--><!--MD5=[f515d4df6c46c2f250b7e9b7c92291ac]
 @startuml
 hide stereotype
 
@@ -87,9 +87,9 @@ rectangle "Target-Focused Workflow" {
     rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
     rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
     ' output files
-    rectangle ".target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
+    rectangle "*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
     ' QC files
-    rectangle ".HSMetrics.txt" as HSMetrics <<QCFile>>
+    rectangle "*HSMetrics.txt" as HSMetrics <<QCFile>>
 }
 
 
@@ -112,8 +112,8 @@ rectangle "Off-Target Workflow" {
     rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>
 
     ' output files
-    rectangle ".target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
-    rectangle ".off-target-dbSNP_depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
+    rectangle "*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
+    rectangle "*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
 
     ' end node
     rectangle "recalibrate-BAM" as RecalBAM #White
@@ -201,8 +201,8 @@ rectangle "Target-Focused Workflow" {
     rectangle "Convert BED to interval.list" as ConvBEDtoIntervalList <<ProcessStep>>
     rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
     rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
-    rectangle ".target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
-    rectangle ".HSMetrics.txt" as HSMetrics <<QCFile>>
+    rectangle "*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
+    rectangle "*HSMetrics.txt" as HSMetrics <<QCFile>>
 }
 
 
@@ -221,8 +221,8 @@ rectangle "Off-Target Workflow" {
     rectangle "Merge with Target File" as MergeWithTarget <<ProcessStep>>
     rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>
 
-    rectangle ".target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
-    rectangle ".off-target-dbSNP_depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
+    rectangle "*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
+    rectangle "*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
 
     rectangle "recalibrate-BAM" as RecalBAM #White
 }

From cfb56ed4fcd9bf3e84d118651d7953be066c5164 Mon Sep 17 00:00:00 2001
From: Nicole Zeltser <nicole.zeltser@gmail.com>
Date: Thu, 21 Mar 2024 19:07:28 -0700
Subject: [PATCH 10/12] fix asterisks in puml labels

---
 docs/calculate-targeted-coverage-flow.puml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/calculate-targeted-coverage-flow.puml b/docs/calculate-targeted-coverage-flow.puml
index fbe24e5..2053078 100644
--- a/docs/calculate-targeted-coverage-flow.puml
+++ b/docs/calculate-targeted-coverage-flow.puml
@@ -25,9 +25,9 @@ rectangle "Target-Focused Workflow" {
     rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
     rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
     ' output files
-    rectangle "*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
+    rectangle "~*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
     ' QC files
-    rectangle "*HSMetrics.txt" as HSMetrics <<QCFile>>
+    rectangle "~*HSMetrics.txt" as HSMetrics <<QCFile>>
 }
 
 
@@ -50,8 +50,8 @@ rectangle "Off-Target Workflow" {
     rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>
 
     ' output files
-    rectangle "*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
-    rectangle "*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
+    rectangle "~*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
+    rectangle "~*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
 
     ' end node
     rectangle "recalibrate-BAM" as RecalBAM #White

From e5185f36c6b69cda3c3cb6111eb3de96b0bbf9f7 Mon Sep 17 00:00:00 2001
From: alkaZeltser <alkaZeltser@users.noreply.github.com>
Date: Fri, 22 Mar 2024 02:09:59 +0000
Subject: [PATCH 11/12] Update SVG images for PlantUML diagrams

---
 docs/calculate-targeted-coverage-flow.svg | 94 +++++++++++------------
 1 file changed, 47 insertions(+), 47 deletions(-)

diff --git a/docs/calculate-targeted-coverage-flow.svg b/docs/calculate-targeted-coverage-flow.svg
index 17857ed..c7b6082 100644
--- a/docs/calculate-targeted-coverage-flow.svg
+++ b/docs/calculate-targeted-coverage-flow.svg
@@ -1,37 +1,37 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="892px" preserveAspectRatio="none" style="width:1359px;height:892px;background:#FFFFFF;" version="1.1" viewBox="0 0 1359 892" width="1359px" zoomAndPan="magnify"><defs/><g><!--MD5=[5793b8a6652117c897ab2de440c96a33]
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="892px" preserveAspectRatio="none" style="width:1355px;height:892px;background:#FFFFFF;" version="1.1" viewBox="0 0 1355 892" width="1355px" zoomAndPan="magnify"><defs/><g><!--MD5=[5793b8a6652117c897ab2de440c96a33]
 cluster Target-Focused Workflow--><g id="cluster_Target-Focused Workflow"><rect height="495" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="512" x="7" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="205" x="160.5" y="21.9951">Target-Focused Workflow</text></g><!--MD5=[d541b56f1a19ef419b51f0e2d36e069b]
 cluster Input1--><g id="cluster_Input1"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="233" x="77" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="193.5" y="52">Input</text></g><!--MD5=[fdf0c65af9cafec17be4ce373e959a1e]
-cluster Off-Target Workflow--><g id="cluster_Off-Target Workflow"><rect height="879" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="606" x="543" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="162" x="765" y="21.9951">Off-Target Workflow</text></g><!--MD5=[fcfe6af240cbb9de2e31d0010bc81b0a]
-cluster Input2--><g id="cluster_Input2"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="343" x="665" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="836.5" y="52">Input</text></g><!--MD5=[f7217341b3bb6bbf768c7f0e049f8d09]
-cluster Legend--><g id="cluster_Legend"><rect height="375" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="180" x="1173" y="31"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="59" x="1233.5" y="45.9951">Legend</text></g><!--MD5=[a83f4c4b109093b6df97f2e5475fbb6d]
+cluster Off-Target Workflow--><g id="cluster_Off-Target Workflow"><rect height="879" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="602" x="543" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="162" x="763" y="21.9951">Off-Target Workflow</text></g><!--MD5=[fcfe6af240cbb9de2e31d0010bc81b0a]
+cluster Input2--><g id="cluster_Input2"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="343" x="664" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="835.5" y="52">Input</text></g><!--MD5=[f7217341b3bb6bbf768c7f0e049f8d09]
+cluster Legend--><g id="cluster_Legend"><rect height="375" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="180" x="1169" y="31"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="59" x="1229.5" y="45.9951">Legend</text></g><!--MD5=[a83f4c4b109093b6df97f2e5475fbb6d]
 entity BAM1--><g id="elem_BAM1"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="355.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="365.5" y="88.9951">BAM</text></g><!--MD5=[afbb0db1cbcdc0e923b4432d737361e0]
 entity ValInputs1--><g id="elem_ValInputs1"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="320.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="330.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b3fc1d5769c32d62159879ccf9acacb3]
 entity CalcReadDepth--><g id="elem_CalcReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="237" x="265.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="217" x="275.5" y="280.9951">Calculate Per-Base Read Depth</text></g><!--MD5=[bd6c7db5d87a2d4a9d8c6ffd88a5bcea]
 entity ConvBEDtoIntervalList--><g id="elem_ConvBEDtoIntervalList"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="202" x="29" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="182" x="39" y="184.9951">Convert BED to interval.list</text></g><!--MD5=[2c5b443c033a35a14a0a2ae3c89dfd10]
 entity ConvtoBED1--><g id="elem_ConvtoBED1"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="321" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="331" y="376.9951">Convert to BED</text></g><!--MD5=[b356e89eaf00e777fdf024a4814b8e18]
 entity CalcCovMetrics--><g id="elem_CalcCovMetrics"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="207" x="23.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="187" x="33.5" y="280.9951">Calculate Coverage Metrics</text></g><!--MD5=[dcd1f042f3b348163f3493299ca35159]
-entity TargetReadDepthBED--><g id="elem_TargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="218" x="275" y="450"/><ellipse cx="290.5" cy="468.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="185" x="298" y="472.9951">target-depth-per-base.bed</text></g><!--MD5=[360be6d182cb7145dcbdee0021c8ccd3]
-entity HSMetrics--><g id="elem_HSMetrics"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="123" x="65.5" y="354"/><ellipse cx="81" cy="372.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="90" x="88.5" y="376.9951">HSMetrics.txt</text></g><!--MD5=[07ce715d8952035f1c648a97cce063ab]
+entity TargetReadDepthBED--><g id="elem_TargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="212" x="278" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="192" x="288" y="472.9951">*target-depth-per-base.bed</text></g><!--MD5=[360be6d182cb7145dcbdee0021c8ccd3]
+entity HSMetrics--><g id="elem_HSMetrics"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="117" x="68.5" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="97" x="78.5" y="376.9951">*HSMetrics.txt</text></g><!--MD5=[07ce715d8952035f1c648a97cce063ab]
 entity TargetFile1--><g id="elem_TargetFile1"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="202" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="212" y="88.9951">Target File</text></g><!--MD5=[bb2b4fcf43ed25e0ab855486922ad703]
 entity BaitFile--><g id="elem_BaitFile"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="73" x="93.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="53" x="103.5" y="88.9951">Bait File</text></g><!--MD5=[3711304ccc2c64bce48f9718f643142e]
-entity ValInputs2--><g id="elem_ValInputs2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="914.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="924.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b6607c3669bb86c4076734be7bd06d49]
-entity CalcReadDepthAtdbSNP--><g id="elem_CalcReadDepthAtdbSNP"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="272" x="844" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="252" x="854" y="280.9951">Cacluate Read Depth at dbSNP Sites</text></g><!--MD5=[5bda774f1e672053773e83dd05eacaed]
-entity FilterReadDepth--><g id="elem_FilterReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="228" x="887" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="208" x="897" y="472.9951">Filter for Minimum Read Depth</text></g><!--MD5=[cd6e518d9ba44279cfc888103d8aa6a4]
-entity FilterOffTarget--><g id="elem_FilterOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="186" x="648" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="166" x="658" y="472.9951">Filter for Off-Target Sites</text></g><!--MD5=[715b69296de685ae7f1f45cea8134010]
-entity ConvtoBED2--><g id="elem_ConvtoBED2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="917" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="927" y="376.9951">Convert to BED</text></g><!--MD5=[0c145ebd8b2b512a07df55d1a2465d38]
-entity AddSlopOffTarget--><g id="elem_AddSlopOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="212" x="921" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="192" x="931" y="568.9951">Add Slop to Off-Target SNPs</text></g><!--MD5=[f50d1513eea2cf224a813b3b0f46f551]
-entity MergeWithTarget--><g id="elem_MergeWithTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="172" x="760" y="642"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="152" x="770" y="664.9951">Merge with Target File</text></g><!--MD5=[6b0d55934776f8df877a4aa9a84c95b4]
-entity AddSlopTarget--><g id="elem_AddSlopTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="209" x="599.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="189" x="609.5" y="280.9951">Add Slop to Target Intervals</text></g><!--MD5=[97b99327512678a3edfd748478556652]
-entity TargetPlusOffTargetReadDepthBED--><g id="elem_TargetPlusOffTargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="334" x="679" y="738"/><ellipse cx="694.5" cy="756.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="301" x="702" y="760.9951">target-with-enriched-off-target-intervals.bed</text></g><!--MD5=[7f5ec864b4cb369ae6c755b0ecd8ff52]
-entity OffTargetReadDepth--><g id="elem_OffTargetReadDepth"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="291" x="595.5" y="546"/><ellipse cx="611" cy="564.7969" fill="#000000" rx="2.5" ry="2.5" style="stroke:#000000;stroke-width:0.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="258" x="618.5" y="568.9951">off-target-dbSNP-depth-per-base.bed</text></g><!--MD5=[e94e62f06dcbdb4a6e54560988436e02]
-entity RecalBAM--><g id="elem_RecalBAM"><rect fill="#FFFFFF" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="128" x="782" y="834"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="108" x="792" y="856.9951">recalibrate-BAM</text></g><!--MD5=[d240438f19e54a6f2cb3889e6527a070]
-entity TargetFile2--><g id="elem_TargetFile2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="681" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="691" y="88.9951">Target File</text></g><!--MD5=[7b92cfaf277f583add5cf6dde83011d4]
-entity dbSNP_VCF--><g id="elem_dbSNP_VCF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="97" x="808.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="77" x="818.5" y="88.9951">dbSNP VCF</text></g><!--MD5=[0b8015d1c6b7568455913bd022baae3a]
-entity BAM2--><g id="elem_BAM2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="940.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="950.5" y="88.9951">BAM</text></g><!--MD5=[486a548dd2b54905abbe5c1ab7fa9983]
-entity IF--><g id="elem_IF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="82" x="1222" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="62" x="1232" y="88.9951">Input File</text></g><!--MD5=[d3ef473a5067122b9254af2bc2f25065]
-entity QC--><g id="elem_QC"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="147" x="1189.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="127" x="1199.5" y="184.9951">Quality Control File</text></g><!--MD5=[633fdf3c843eeff0d0fbc3bde364bced]
-entity OF--><g id="elem_OF"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="95" x="1215.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="75" x="1225.5" y="280.9951">Output File</text></g><!--MD5=[7842cb4300efb401920d8f72ebe921e6]
-entity PS--><g id="elem_PS"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="112" x="1207" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="92" x="1217" y="376.9951">Process Step</text></g><!--MD5=[4ebbafa84b39c454a0f1728fb61efbcb]
+entity ValInputs2--><g id="elem_ValInputs2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="913.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="923.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b6607c3669bb86c4076734be7bd06d49]
+entity CalcReadDepthAtdbSNP--><g id="elem_CalcReadDepthAtdbSNP"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="272" x="843" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="252" x="853" y="280.9951">Cacluate Read Depth at dbSNP Sites</text></g><!--MD5=[5bda774f1e672053773e83dd05eacaed]
+entity FilterReadDepth--><g id="elem_FilterReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="228" x="884" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="208" x="894" y="472.9951">Filter for Minimum Read Depth</text></g><!--MD5=[cd6e518d9ba44279cfc888103d8aa6a4]
+entity FilterOffTarget--><g id="elem_FilterOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="186" x="646" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="166" x="656" y="472.9951">Filter for Off-Target Sites</text></g><!--MD5=[715b69296de685ae7f1f45cea8134010]
+entity ConvtoBED2--><g id="elem_ConvtoBED2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="916" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="926" y="376.9951">Convert to BED</text></g><!--MD5=[0c145ebd8b2b512a07df55d1a2465d38]
+entity AddSlopOffTarget--><g id="elem_AddSlopOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="212" x="917" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="192" x="927" y="568.9951">Add Slop to Off-Target SNPs</text></g><!--MD5=[f50d1513eea2cf224a813b3b0f46f551]
+entity MergeWithTarget--><g id="elem_MergeWithTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="172" x="758" y="642"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="152" x="768" y="664.9951">Merge with Target File</text></g><!--MD5=[6b0d55934776f8df877a4aa9a84c95b4]
+entity AddSlopTarget--><g id="elem_AddSlopTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="209" x="598.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="189" x="608.5" y="280.9951">Add Slop to Target Intervals</text></g><!--MD5=[97b99327512678a3edfd748478556652]
+entity TargetPlusOffTargetReadDepthBED--><g id="elem_TargetPlusOffTargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="328" x="680" y="738"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="308" x="690" y="760.9951">*target-with-enriched-off-target-intervals.bed</text></g><!--MD5=[7f5ec864b4cb369ae6c755b0ecd8ff52]
+entity OffTargetReadDepth--><g id="elem_OffTargetReadDepth"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="285" x="596.5" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="265" x="606.5" y="568.9951">*off-target-dbSNP-depth-per-base.bed</text></g><!--MD5=[e94e62f06dcbdb4a6e54560988436e02]
+entity RecalBAM--><g id="elem_RecalBAM"><rect fill="#FFFFFF" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="128" x="780" y="834"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="108" x="790" y="856.9951">recalibrate-BAM</text></g><!--MD5=[d240438f19e54a6f2cb3889e6527a070]
+entity TargetFile2--><g id="elem_TargetFile2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="680" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="690" y="88.9951">Target File</text></g><!--MD5=[7b92cfaf277f583add5cf6dde83011d4]
+entity dbSNP_VCF--><g id="elem_dbSNP_VCF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="97" x="807.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="77" x="817.5" y="88.9951">dbSNP VCF</text></g><!--MD5=[0b8015d1c6b7568455913bd022baae3a]
+entity BAM2--><g id="elem_BAM2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="939.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="949.5" y="88.9951">BAM</text></g><!--MD5=[486a548dd2b54905abbe5c1ab7fa9983]
+entity IF--><g id="elem_IF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="82" x="1218" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="62" x="1228" y="88.9951">Input File</text></g><!--MD5=[d3ef473a5067122b9254af2bc2f25065]
+entity QC--><g id="elem_QC"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="147" x="1185.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="127" x="1195.5" y="184.9951">Quality Control File</text></g><!--MD5=[633fdf3c843eeff0d0fbc3bde364bced]
+entity OF--><g id="elem_OF"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="95" x="1211.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="75" x="1221.5" y="280.9951">Output File</text></g><!--MD5=[7842cb4300efb401920d8f72ebe921e6]
+entity PS--><g id="elem_PS"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="112" x="1203" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="92" x="1213" y="376.9951">Process Step</text></g><!--MD5=[4ebbafa84b39c454a0f1728fb61efbcb]
 link BAM1 to ValInputs1--><g id="link_BAM1_ValInputs1"><path d="M381,102.24 C381,117.48 381,139.81 381,156.46 " fill="none" id="BAM1-to-ValInputs1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="381,161.87,385,152.87,381,156.87,377,152.87,381,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0b188298c9b1afe471d4865e17af690e]
 link BaitFile to ConvBEDtoIntervalList--><g id="link_BaitFile_ConvBEDtoIntervalList"><path d="M130,102.24 C130,117.48 130,139.81 130,156.46 " fill="none" id="BaitFile-to-ConvBEDtoIntervalList" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="130,161.87,134,152.87,130,156.87,126,152.87,130,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[a98f2fcb5fff3f38e9b30ea7ce7944cc]
 reverse link BaitFile to TargetFile1--><g id="link_BaitFile_TargetFile1"><path d="M172.05,84 C181.94,84 191.84,84 201.73,84 " fill="none" id="BaitFile-backto-TargetFile1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="166.88,84,175.8914,87.9743,171.88,83.9857,175.8685,79.9743,166.88,84" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[8613a7106181726335c268ad9afcbade]
@@ -43,23 +43,23 @@ link ValInputs1 to CalcCovMetrics--><g id="link_ValInputs1_CalcCovMetrics"><path
 link CalcCovMetrics to HSMetrics--><g id="link_CalcCovMetrics_HSMetrics"><path d="M127,294.24 C127,309.48 127,331.81 127,348.46 " fill="none" id="CalcCovMetrics-to-HSMetrics" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="127,353.87,131,344.87,127,348.87,123,344.87,127,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[01f923ac9ec9e6500d1bb9fa79e1697e]
 link CalcReadDepth to ConvtoBED1--><g id="link_CalcReadDepth_ConvtoBED1"><path d="M384,294.24 C384,309.48 384,331.81 384,348.46 " fill="none" id="CalcReadDepth-to-ConvtoBED1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="384,353.87,388,344.87,384,348.87,380,344.87,384,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[af6509568e048ae4cd4a149100a354eb]
 link ConvtoBED1 to TargetReadDepthBED--><g id="link_ConvtoBED1_TargetReadDepthBED"><path d="M384,390.24 C384,405.48 384,427.81 384,444.46 " fill="none" id="ConvtoBED1-to-TargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="384,449.87,388,440.87,384,444.87,380,440.87,384,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ad70a8f2d24c7fbe93a363248ba8fd89]
-link TargetFile2 to AddSlopTarget--><g id="link_TargetFile2_AddSlopTarget"><path d="M724.92,102.2 C720.74,136.67 711.36,214.23 706.71,252.61 " fill="none" id="TargetFile2-to-AddSlopTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="706.06,257.98,711.1096,249.5241,706.6591,253.016,703.1672,248.5656,706.06,257.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bb9b1f52b6b7f984ba4d3d204d33fcda]
-link TargetFile2 to MergeWithTarget--><g id="link_TargetFile2_MergeWithTarget"><path d="M695.2,102.22 C646.74,131.05 560,193.97 560,275 C560,275 560,275 560,469 C560,519.86 544.3,543.92 578,582 C601.61,608.67 686.64,630.13 754.67,643.55 " fill="none" id="TargetFile2-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="759.95,644.58,751.8807,638.9332,755.0422,643.6241,750.3513,646.7856,759.95,644.58" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0f5f9f541059e0d392cad8edec1088b0]
-link dbSNP_VCF to CalcReadDepthAtdbSNP--><g id="link_dbSNP_VCF_CalcReadDepthAtdbSNP"><path d="M860.38,102.24 C865.52,125.46 876.88,167.39 897,198 C911.66,220.29 934.1,240.59 951.96,254.75 " fill="none" id="dbSNP_VCF-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="955.93,257.85,951.3077,249.1532,951.9925,254.7685,946.3772,255.4532,955.93,257.85" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1085dcdb1e044111634ab5f4c085fbb6]
-link BAM2 to ValInputs2--><g id="link_BAM2_ValInputs2"><path d="M967.65,102.24 C969.12,117.61 971.28,140.2 972.88,156.89 " fill="none" id="BAM2-to-ValInputs2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="973.36,161.87,976.4685,152.5246,972.8752,156.8936,968.5062,153.3003,973.36,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[26102ab38cefa976c6f11175f31d78b3]
-link ValInputs2 to CalcReadDepthAtdbSNP--><g id="link_ValInputs2_CalcReadDepthAtdbSNP"><path d="M975.92,198.24 C976.73,213.48 977.92,235.81 978.8,252.46 " fill="none" id="ValInputs2-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="979.09,257.87,982.5948,248.6659,978.8182,252.8774,974.6067,249.1008,979.09,257.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bc906825f7e1d5b70f40674632bccb60]
-link AddSlopTarget to FilterOffTarget--><g id="link_AddSlopTarget_FilterOffTarget"><path d="M707.35,294.2 C714.06,328.67 729.17,406.23 736.64,444.61 " fill="none" id="AddSlopTarget-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="737.69,449.98,739.8956,440.3813,736.7341,445.0722,732.0432,441.9107,737.69,449.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[e6ec3830f61b2fc00c1f964c6c082250]
-link CalcReadDepthAtdbSNP to ConvtoBED2--><g id="link_CalcReadDepthAtdbSNP_ConvtoBED2"><path d="M980,294.24 C980,309.48 980,331.81 980,348.46 " fill="none" id="CalcReadDepthAtdbSNP-to-ConvtoBED2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="980,353.87,984,344.87,980,348.87,976,344.87,980,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[312c39a7f5e428ae64e27424907166bd]
-link ConvtoBED2 to FilterOffTarget--><g id="link_ConvtoBED2_FilterOffTarget"><path d="M936.72,390.02 C895.14,406.38 832.44,431.04 789.26,448.02 " fill="none" id="ConvtoBED2-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="784.36,449.95,794.2008,450.3475,789.0073,448.1054,791.2494,442.9118,784.36,449.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ea959455ce9951d3e4721f89ee60932b]
-link ConvtoBED2 to FilterReadDepth--><g id="link_ConvtoBED2_FilterReadDepth"><path d="M983.85,390.24 C987.29,405.61 992.33,428.2 996.06,444.89 " fill="none" id="ConvtoBED2-to-FilterReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="997.17,449.87,999.1224,440.2166,996.0853,444.9891,991.3129,441.952,997.17,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0e0a99d1d7bc0797a534b161d1c3fca8]
-link FilterReadDepth to AddSlopOffTarget--><g id="link_FilterReadDepth_AddSlopOffTarget"><path d="M1005.77,486.24 C1010.02,501.61 1016.27,524.2 1020.88,540.89 " fill="none" id="FilterReadDepth-to-AddSlopOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="1022.26,545.87,1023.7023,536.1273,1020.9203,541.0528,1015.9948,538.2708,1022.26,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1fe930d4fe042d6de6dd8d043965d9f2]
-link FilterOffTarget to OffTargetReadDepth--><g id="link_FilterOffTarget_OffTargetReadDepth"><path d="M741,486.24 C741,501.48 741,523.81 741,540.46 " fill="none" id="FilterOffTarget-to-OffTargetReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="741,545.87,745,536.87,741,540.87,737,536.87,741,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[be633c3fef0ea7de7d91abfc3ce66e7d]
-link AddSlopOffTarget to MergeWithTarget--><g id="link_AddSlopOffTarget_MergeWithTarget"><path d="M994.22,582.02 C963.05,598.21 916.21,622.54 883.55,639.5 " fill="none" id="AddSlopOffTarget-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="878.84,641.95,888.6707,641.3517,883.2773,639.6455,884.9835,634.2521,878.84,641.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0fa50402f24eb397243c00d2dc3ff62f]
-link MergeWithTarget to TargetPlusOffTargetReadDepthBED--><g id="link_MergeWithTarget_TargetPlusOffTargetReadDepthBED"><path d="M846,678.24 C846,693.48 846,715.81 846,732.46 " fill="none" id="MergeWithTarget-to-TargetPlusOffTargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="846,737.87,850,728.87,846,732.87,842,728.87,846,737.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[4737fbc0abd4b31898a08a11d07ff5b8]
-link TargetPlusOffTargetReadDepthBED to RecalBAM--><g id="link_TargetPlusOffTargetReadDepthBED_RecalBAM"><path d="M846,774.24 C846,789.48 846,811.81 846,828.46 " fill="none" id="TargetPlusOffTargetReadDepthBED-to-RecalBAM" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="846,833.87,850,824.87,846,828.87,842,824.87,846,833.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1d4d0dbdd50de0a0980321eccab73fac]
+link TargetFile2 to AddSlopTarget--><g id="link_TargetFile2_AddSlopTarget"><path d="M723.92,102.2 C719.74,136.67 710.36,214.23 705.71,252.61 " fill="none" id="TargetFile2-to-AddSlopTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="705.06,257.98,710.1096,249.5241,705.6591,253.016,702.1672,248.5656,705.06,257.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bb9b1f52b6b7f984ba4d3d204d33fcda]
+link TargetFile2 to MergeWithTarget--><g id="link_TargetFile2_MergeWithTarget"><path d="M694.78,102.04 C646.69,130.83 560,193.97 560,275 C560,275 560,275 560,469 C560,519.93 545.14,543.96 579,582 C622.37,630.72 694.55,649.4 752.64,656.21 " fill="none" id="TargetFile2-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="757.86,656.79,749.3615,651.8125,752.8911,656.2331,748.4705,659.7628,757.86,656.79" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0f5f9f541059e0d392cad8edec1088b0]
+link dbSNP_VCF to CalcReadDepthAtdbSNP--><g id="link_dbSNP_VCF_CalcReadDepthAtdbSNP"><path d="M859.38,102.24 C864.52,125.46 875.88,167.39 896,198 C910.66,220.29 933.1,240.59 950.96,254.75 " fill="none" id="dbSNP_VCF-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="954.93,257.85,950.3077,249.1532,950.9925,254.7685,945.3772,255.4532,954.93,257.85" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1085dcdb1e044111634ab5f4c085fbb6]
+link BAM2 to ValInputs2--><g id="link_BAM2_ValInputs2"><path d="M966.65,102.24 C968.12,117.61 970.28,140.2 971.88,156.89 " fill="none" id="BAM2-to-ValInputs2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="972.36,161.87,975.4685,152.5246,971.8752,156.8936,967.5062,153.3003,972.36,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[26102ab38cefa976c6f11175f31d78b3]
+link ValInputs2 to CalcReadDepthAtdbSNP--><g id="link_ValInputs2_CalcReadDepthAtdbSNP"><path d="M974.92,198.24 C975.73,213.48 976.92,235.81 977.8,252.46 " fill="none" id="ValInputs2-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="978.09,257.87,981.5948,248.6659,977.8182,252.8774,973.6067,249.1008,978.09,257.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bc906825f7e1d5b70f40674632bccb60]
+link AddSlopTarget to FilterOffTarget--><g id="link_AddSlopTarget_FilterOffTarget"><path d="M706.26,294.2 C712.79,328.67 727.49,406.23 734.76,444.61 " fill="none" id="AddSlopTarget-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="735.78,449.98,738.0394,440.3938,734.8517,445.0669,730.1785,441.8792,735.78,449.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[e6ec3830f61b2fc00c1f964c6c082250]
+link CalcReadDepthAtdbSNP to ConvtoBED2--><g id="link_CalcReadDepthAtdbSNP_ConvtoBED2"><path d="M979,294.24 C979,309.48 979,331.81 979,348.46 " fill="none" id="CalcReadDepthAtdbSNP-to-ConvtoBED2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="979,353.87,983,344.87,979,348.87,975,344.87,979,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[312c39a7f5e428ae64e27424907166bd]
+link ConvtoBED2 to FilterOffTarget--><g id="link_ConvtoBED2_FilterOffTarget"><path d="M935.54,390.02 C893.7,406.41 830.56,431.14 787.2,448.12 " fill="none" id="ConvtoBED2-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="782.54,449.95,792.3793,450.384,787.1941,448.1226,789.4555,442.9374,782.54,449.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ea959455ce9951d3e4721f89ee60932b]
+link ConvtoBED2 to FilterReadDepth--><g id="link_ConvtoBED2_FilterReadDepth"><path d="M982.48,390.24 C985.59,405.61 990.16,428.2 993.53,444.89 " fill="none" id="ConvtoBED2-to-FilterReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="994.54,449.87,996.6865,440.2579,993.5539,444.9682,988.8436,441.8356,994.54,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0e0a99d1d7bc0797a534b161d1c3fca8]
+link FilterReadDepth to AddSlopOffTarget--><g id="link_FilterReadDepth_AddSlopOffTarget"><path d="M1002.59,486.24 C1006.67,501.61 1012.68,524.2 1017.12,540.89 " fill="none" id="FilterReadDepth-to-AddSlopOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="1018.44,545.87,1019.9896,536.1438,1017.1535,541.0384,1012.2589,538.2023,1018.44,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1fe930d4fe042d6de6dd8d043965d9f2]
+link FilterOffTarget to OffTargetReadDepth--><g id="link_FilterOffTarget_OffTargetReadDepth"><path d="M739,486.24 C739,501.48 739,523.81 739,540.46 " fill="none" id="FilterOffTarget-to-OffTargetReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="739,545.87,743,536.87,739,540.87,735,536.87,739,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[be633c3fef0ea7de7d91abfc3ce66e7d]
+link AddSlopOffTarget to MergeWithTarget--><g id="link_AddSlopOffTarget_MergeWithTarget"><path d="M990.58,582.02 C959.76,598.21 913.43,622.54 881.14,639.5 " fill="none" id="AddSlopOffTarget-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="876.48,641.95,886.3075,641.3019,880.9055,639.623,882.5844,634.221,876.48,641.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0fa50402f24eb397243c00d2dc3ff62f]
+link MergeWithTarget to TargetPlusOffTargetReadDepthBED--><g id="link_MergeWithTarget_TargetPlusOffTargetReadDepthBED"><path d="M844,678.24 C844,693.48 844,715.81 844,732.46 " fill="none" id="MergeWithTarget-to-TargetPlusOffTargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="844,737.87,848,728.87,844,732.87,840,728.87,844,737.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[4737fbc0abd4b31898a08a11d07ff5b8]
+link TargetPlusOffTargetReadDepthBED to RecalBAM--><g id="link_TargetPlusOffTargetReadDepthBED_RecalBAM"><path d="M844,774.24 C844,789.48 844,811.81 844,828.46 " fill="none" id="TargetPlusOffTargetReadDepthBED-to-RecalBAM" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="844,833.87,848,824.87,844,828.87,840,824.87,844,833.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1d4d0dbdd50de0a0980321eccab73fac]
 link IF to QC--><!--MD5=[03c241bed99ac1776e7d8c4bd4f5cca5]
 link QC to OF--><!--MD5=[35700df3515afd241139af4c0386ffe2]
-link OF to PS--><!--MD5=[f515d4df6c46c2f250b7e9b7c92291ac]
+link OF to PS--><!--MD5=[b8e815e99e79e7c975214b5ce20b9ed4]
 @startuml
 hide stereotype
 
@@ -87,9 +87,9 @@ rectangle "Target-Focused Workflow" {
     rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
     rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
     ' output files
-    rectangle "*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
+    rectangle "~*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
     ' QC files
-    rectangle "*HSMetrics.txt" as HSMetrics <<QCFile>>
+    rectangle "~*HSMetrics.txt" as HSMetrics <<QCFile>>
 }
 
 
@@ -112,8 +112,8 @@ rectangle "Off-Target Workflow" {
     rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>
 
     ' output files
-    rectangle "*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
-    rectangle "*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
+    rectangle "~*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
+    rectangle "~*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
 
     ' end node
     rectangle "recalibrate-BAM" as RecalBAM #White
@@ -201,8 +201,8 @@ rectangle "Target-Focused Workflow" {
     rectangle "Convert BED to interval.list" as ConvBEDtoIntervalList <<ProcessStep>>
     rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
     rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
-    rectangle "*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
-    rectangle "*HSMetrics.txt" as HSMetrics <<QCFile>>
+    rectangle "~*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
+    rectangle "~*HSMetrics.txt" as HSMetrics <<QCFile>>
 }
 
 
@@ -221,8 +221,8 @@ rectangle "Off-Target Workflow" {
     rectangle "Merge with Target File" as MergeWithTarget <<ProcessStep>>
     rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>
 
-    rectangle "*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
-    rectangle "*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
+    rectangle "~*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
+    rectangle "~*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>
 
     rectangle "recalibrate-BAM" as RecalBAM #White
 }

From 571eb2af273e18b6fefab1aee1f180a61572bc42 Mon Sep 17 00:00:00 2001
From: Yash Patel <yashpatel@mednet.ucla.edu>
Date: Fri, 22 Mar 2024 12:01:54 -0700
Subject: [PATCH 12/12] Empty commit