draft API docs for BWA and strelka

2 files changed, 35 insertions, 5 deletions

diff --git a/tools/bwa.nix b/tools/bwa.nix
index d0ab5ee..03735d1 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -2,7 +2,16 @@
 
 with bionix;
 
-{
-  align = callBionixE ./bwa-mem.nix;
+rec {
+  /* Align read against a reference: defaults to bwa-mem */
+  align = bwa-mem;
+
+  /* Align reads against a reference using bwa-mem
+  Type: bwa-mem :: {ref = fasta, bamOutput = bool, ...} -> {input1, input2} -> bam/sam
+  */
+  bwa-mem = callBionixE ./bwa-mem.nix;
+  /* Creates an reference index for BWA
+  Type: {...} -> fasta -> BWA index
+  */
   index = callBionixE ./bwa-index.nix;
 }
diff --git a/tools/strelka.nix b/tools/strelka.nix
index 9a8f1aa..1cf8961 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -4,21 +4,42 @@ with bionix;
 with types;
 
 {
+  /* Calls somatic variants
+  Type: callSomatic :: {...} -> {tumour, normal} -> somatic results
+  */
   callSomatic = callBionixE ./strelka-callSomatic.nix;
+  /* Calls variants
+  Type: call :: {...} -> [input] -> results
+  */
   call = callBionixE ./strelka-call.nix;
-  variants = drv: stage {
+  /* Extract VCF file from results
+  Type: variants :: results -> vcf
+  */
+  variants =
+    # result of call
+    drv: stage {
     name = "strelka-call-variants";
     buildCommand = ''
       ln -s ${drv}/variants/variants.vcf.gz $out
     '';
     passthru.filetype = filetype.gz (filetype.vcf {ref=ref;});
   };
-  indels = drv: stage {
+  /* Extract indels from somatic results
+  Type: indels :: somatic results -> vcf
+  */
+  indels =
+    # result of callSomatic
+    drv: stage {
     name = "strelka-callVariants-indels";
     buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf.gz $out";
     passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});
   };
-  snvs = drv: stage {
+  /* Extract SNVs from somatic results
+  Type: snvs :: somatic results -> vcf
+  */
+  snvs =
+    # result of callSomatic
+    drv: stage {
     name = "strelka-callVariants-snvs";
     buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf.gz $out";
     passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});