2 files changed, 45 insertions, 2 deletions
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);
 }