From c7756678c8a543f216654d518eeee3c4bd6a4b8f Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 3 Feb 2021 11:49:23 +1100
Subject: add inline documentation

---
 tools/delly.nix      |  3 +++
 tools/fastp.nix      |  4 ++++
 tools/gridss.nix     |  4 ++--
 tools/kallisto.nix   |  4 ++++
 tools/last.nix       |  3 +++
 tools/lumpy.nix      |  3 +++
 tools/manta.nix      |  3 +++
 tools/mosdepth.nix   |  7 +++++++
 tools/mutect.nix     |  4 ++++
 tools/octopus.nix    |  7 +++++++
 tools/picard.nix     |  3 +++
 tools/platypus.nix   |  3 +++
 tools/sambamba.nix   | 23 +++++++++++++++++++++++
 tools/snpeff.nix     |  7 +++++++
 tools/snver.nix      |  3 +++
 tools/star.nix       |  3 +++
 tools/whisper.nix    |  4 ++++
 tools/xenomapper.nix |  3 +++
 18 files changed, 89 insertions(+), 2 deletions(-)

(limited to 'tools')

diff --git a/tools/delly.nix b/tools/delly.nix
index 9bac4c6..d94457c 100644
--- a/tools/delly.nix
+++ b/tools/delly.nix
@@ -3,5 +3,8 @@
 with bionix;
 
 {
+  /* Call structural variants
+  Type: call { ... } -> [bam] -> vcf
+  */
   call = callBionixE ./delly-call.nix;
 }
diff --git a/tools/fastp.nix b/tools/fastp.nix
index 90f6c1d..551d270 100644
--- a/tools/fastp.nix
+++ b/tools/fastp.nix
@@ -4,6 +4,10 @@ with bionix;
 
 rec {
     app = pkgs.callPackage ./fastp-app.nix {};
+
+    /* Check and filter fastqs
+    Type: { ... } -> { input1, input2 ? null } -> { out :: html, fastq1 :: fastq, fastq2 :: fastq, json :: JSON } 
+    */
     check = callBionixE ./fastp-check.nix;
 }
 
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 28af089..9e30dea 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -72,8 +72,8 @@ rec {
       (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 SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual tools above.
+  Type: call :: [bam] -> GRIDSS result
   */
   call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs);
 
diff --git a/tools/kallisto.nix b/tools/kallisto.nix
index 31e15d9..13de61e 100644
--- a/tools/kallisto.nix
+++ b/tools/kallisto.nix
@@ -4,5 +4,9 @@ with bionix;
 
 {
   index = callBionixE ./kallisto-index.nix;
+
+  /* Quantify reads against a transcriptome
+  Type: { bias :: bool, bootstrapSamples :: int, seed :: int, plaintext :: bool, fusion :: bool, single :: bool, frStranded :: bool, rfStranded :: bool, fragmentLength :: Int, fragmentSD :: real } -> [fastq] -> kallisto
+  */
   quant = callBionixE ./kallisto-quant.nix;
 }
diff --git a/tools/last.nix b/tools/last.nix
index 4e40a65..3755bde 100644
--- a/tools/last.nix
+++ b/tools/last.nix
@@ -3,6 +3,9 @@
 with bionix;
 
 rec {
+  /* Align reads against a reference genome
+  Type: { ref :: fastq, ... } -> { input1, input2} -> last
+  */
   align = callBionixE ./last-align.nix;
   index = callBionixE ./last-index.nix;
 }
diff --git a/tools/lumpy.nix b/tools/lumpy.nix
index 0894054..f82134e 100644
--- a/tools/lumpy.nix
+++ b/tools/lumpy.nix
@@ -3,5 +3,8 @@
 with bionix;
 
 {
+  /* Call structural variants
+  Type: { ... } -> [bam] -> vcf
+  */
   call = callBionixE ./lumpy-call.nix;
 }
diff --git a/tools/manta.nix b/tools/manta.nix
index 8136fa7..b34753f 100644
--- a/tools/manta.nix
+++ b/tools/manta.nix
@@ -3,5 +3,8 @@
 with bionix;
 
 {
+  /* Call structural variants
+  Type: { ... } -> { normals :: [bam], tumour :: bam } -> manta
+  */
   call = callBionixE ./manta-call.nix;
 }
diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix
index a5083a7..cbebdfb 100644
--- a/tools/mosdepth.nix
+++ b/tools/mosdepth.nix
@@ -3,6 +3,13 @@
 with bionix;
 
 {
+  /* Compute coverage of a reference given an alignemnt
+  Type: { ... } -> bam -> mosdepth
+  */
   depth = callBionixE ./mosdepth-depth.nix;
+
+  /* Plot sample coverages. Names are optional.
+  Type: { ... } -> { inputs :: [mosdepth], names :: [string] } -> html
+  */
   plot = callBionixE ./mosdepth-plot.nix;
 }
diff --git a/tools/mutect.nix b/tools/mutect.nix
index 54a9fac..addea77 100644
--- a/tools/mutect.nix
+++ b/tools/mutect.nix
@@ -4,5 +4,9 @@ with bionix;
 
 {
   app = pkgs.callPackage ./mutect-app.nix {};
+
+  /* Call somatic variants with mutect
+  Type: { cosmic, dbsnp, ... } -> { normal :: bam, tumour :: bam } -> vcf
+  */
   call = callBionixE ./mutect-call.nix;
 }
diff --git a/tools/octopus.nix b/tools/octopus.nix
index 4d0c7f6..858d133 100644
--- a/tools/octopus.nix
+++ b/tools/octopus.nix
@@ -3,6 +3,13 @@
 with bionix;
 
 {
+  /* Call variants for a population
+  Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> [bam] -> vcf
+  */
   call = callBionixE ./octopus-call.nix;
+   
+  /* Call somatic variants
+  Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> { normal :: bam, tumours :: [bam] } -> vcf
+  */
   callSomatic = callBionixE ./octopus-callSomatic.nix;
 }
diff --git a/tools/picard.nix b/tools/picard.nix
index 551995f..4246afe 100644
--- a/tools/picard.nix
+++ b/tools/picard.nix
@@ -3,5 +3,8 @@
 with bionix;
 
 {
+    /* Mark duplicates
+    Type: { ... } -> bam -> bam
+    */
     markDuplicates = callBionixE ./picard-markDuplicates.nix;
 }
\ No newline at end of file
diff --git a/tools/platypus.nix b/tools/platypus.nix
index 4379675..c93a2d8 100644
--- a/tools/platypus.nix
+++ b/tools/platypus.nix
@@ -3,5 +3,8 @@
 with bionix;
 
 {
+  /* Call variants 
+  Type: { ... } -> [bam] -> vcf
+  */
   call = callBionixE ./platypus-callVariants.nix;
 }
diff --git a/tools/sambamba.nix b/tools/sambamba.nix
index 552e6e3..3c1d1fd 100644
--- a/tools/sambamba.nix
+++ b/tools/sambamba.nix
@@ -6,10 +6,33 @@ let
   gen = callBionixE ./sambamba-generic.nix;
 
 in {
+  /* Sort aligned reads
+  Type: { nameSort :: bool, ... } -> bam -> bam
+  */
   sort = callBionixE ./sambamba-sort.nix;
+
+  /* Build an index
+  Type: { ... } -> bam -> index
+  */
   index = def gen {tool = "index"; };
+
+  /* Merge bam files
+  Type: { ... } -> [bam] -> bam
+  */
   merge = def gen {tool = "merge"; };
+
+  /* Slice a region out of a bam file
+  Type: { region, ... } -> bam -> bam
+  */
   slice = def gen {tool = "slice"; };
+
+  /* Compute flag statistics
+  Type: { ... } -> bam -> flagstat
+  */
   flagstat = def gen {tool = "flagstat"; };
+
+  /* Mark duplicates
+  Type: { ... } -> bam -> bam
+  */
   markdup = def gen {tool = "markdup"; };
 }
diff --git a/tools/snpeff.nix b/tools/snpeff.nix
index c5ef04d..fb3f4a9 100644
--- a/tools/snpeff.nix
+++ b/tools/snpeff.nix
@@ -3,6 +3,13 @@
 with bionix;
 
 {
+  /* Annotate variants with SNPEff database. Some annotation DBs available in bionix.ref (e.g., bionix.ref.grch38.snpeff.db).
+  Type: { db, ... } -> vcf -> vcf
+  */
   annotate = callBionixE ./snpeff-annotate.nix;
+  
+  /* Annotate variants with dbNSFP database. Some dbNSFP annotation DBs available in bionix.ref (e.g., bionix.ref.grch38.snpeff.dbNSFP).
+  Type: { dbnsfp, ... } -> vcf -> vcf
+  */
   dbnsfp = callBionixE ./snpeff-dbnsfp.nix;
 }
diff --git a/tools/snver.nix b/tools/snver.nix
index 7c84777..6f95e1b 100644
--- a/tools/snver.nix
+++ b/tools/snver.nix
@@ -6,5 +6,8 @@ with pkgs;
 {
   app = callPackage ./snver-app.nix {};
 
+  /* Call variants
+  Type: { ploidy, ... } -> [bam] -> vcf
+  */
   call = callBionix ./snver-call.nix;
 }
diff --git a/tools/star.nix b/tools/star.nix
index a0a2d58..744c4e0 100644
--- a/tools/star.nix
+++ b/tools/star.nix
@@ -3,6 +3,9 @@
 with bionix;
 
 {
+  /* Align RNA against a reference genome
+  Type: { ref, ... } -> { input1, input2 } -> bam
+  */
   align = callBionixE ./star-align.nix;
   index = callBionixE ./star-index.nix;
 }
diff --git a/tools/whisper.nix b/tools/whisper.nix
index b729675..ff56f8a 100644
--- a/tools/whisper.nix
+++ b/tools/whisper.nix
@@ -4,5 +4,9 @@ with bionix;
 
 rec {
   index = callBionixE ./whisper-index.nix;
+
+  /* Align reads against a reference
+  Type: { ref, ... } -> { input1, input2 } -> bam
+  */
   align = callBionixE ./whisper-align.nix;
 }
diff --git a/tools/xenomapper.nix b/tools/xenomapper.nix
index 8247e25..d22f84b 100644
--- a/tools/xenomapper.nix
+++ b/tools/xenomapper.nix
@@ -3,5 +3,8 @@
 with bionix;
 
 {
+  /* Split aligned reads based on primary and secondary alignments
+  Type: { ... } -> { primary :: bam, secondary :: bam } -> { primary_specific :: bam, primary_multi :: bam, secondary_specific :: bam, secondary_multi :: bam, unassigned :: bam, unresolved :: bam }
+  */
   allocate = callBionixE ./xenomapper-allocate.nix;
 }
\ No newline at end of file
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