From a0cb745ca7a0c1bdfef31fa1489384273774cb4d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 6 Mar 2019 13:52:56 +1100
Subject: api docs: init GRIDSS

---
 doc/tools-doc.nix               |  1 +
 doc/tools.xml                   |  1 +
 tools/gridss-computeSamTags.nix |  1 -
 tools/gridss.nix                | 46 ++++++++++++++++++++++++++++++++++++++++-
 4 files changed, 47 insertions(+), 2 deletions(-)

diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
index f52f6ad..d68a6b1 100644
--- a/doc/tools-doc.nix
+++ b/doc/tools-doc.nix
@@ -30,6 +30,7 @@ stage {
     docgen cnvkit 'CNVkit CNV caller'
     docgen facets 'Facets CNV caller'
     docgen fastqc 'FastQC quality control'
+    docgen gridss 'GRIDSS SV caller'
     docgen strelka 'Strelka2 variant caller'
 
     mkdir $out
diff --git a/doc/tools.xml b/doc/tools.xml
index 2592b48..022aa3f 100644
--- a/doc/tools.xml
+++ b/doc/tools.xml
@@ -14,6 +14,7 @@
   <xi:include href="cnvkit.xml" />
   <xi:include href="facets.xml" />
   <xi:include href="fastqc.xml" />
+  <xi:include href="gridss.xml" />
   <xi:include href="strelka.xml" />
  </section>
 </book>
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index 5b249e7..5e35749 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -1,5 +1,4 @@
 { bionix
-, blacklist ? null
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
diff --git a/tools/gridss.nix b/tools/gridss.nix
index e8dd304..7148220 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -7,15 +7,55 @@ rec {
     url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
-  genConfig = callBionixE ./gridss-configFile.nix {};
+
+  /* Generate configuration file for GRIDSS. Takes attribute sets to GRIDSS ini style format.
+  Type: genConfig :: attrSet -> ini file
+  */
+  genConfig = callBionix ./gridss-configFile.nix {};
+
+  /* Invoke the callVariants tool
+  Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants
+  */
   callVariants = callBionixE ./gridss-callVariants.nix;
+
+  /* Invoke computeSamTags tool
+  Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam
+  */
   computeSamTags = callBionixE ./gridss-computeSamTags.nix;
+
+  /* Invoke softClipsToSplitReads tool
+  Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam
+  */
   softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;
+
+  /* Invoke collectMetrics tool
+  Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics
+  */
   collectMetrics = callBionixE ./gridss-collectMetrics.nix;
+
+  /* Invoke extractSVReads tool
+  Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam
+  */
   extractSVReads = callBionixE ./gridss-extractSVReads.nix;
+
+  /* Invoke assembly tool
+  Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam
+  */
   assemble = callBionixE ./gridss-assemble.nix;
+
+  /* Invoke identifyVariants tool
+  Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
+  */
   identifyVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify);
+
+  /* Invoke annotateVariants tool
+  Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
+  */
   annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
+
+  /* Preprocess BAM files to extract SV reads and convert soft clips to split reads
+  Type: preprocessBam :: bam -> bam
+  */
   preprocessBam = with samtools;
     pipe [
       (gridss.extractSVReads {})
@@ -24,5 +64,9 @@ rec {
       (gridss.softClipsToSplitReads {})
       (sort {})
     ];
+
+  /* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual above tools.
+  Type: [bam] -> GRIDSS result
+  */
   call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs);
 }
-- 
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