Add flagstat and fastqc

1 files changed, 9 insertions, 0 deletions

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 31570ee..ef2af1b 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -6,6 +6,8 @@ let
   ref = ./example/ref.fa;
   alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = samtools.sort { };
+  flagstat = samtools.flagstat {};
+  check = fastqc.check {};
   callVariants = strelka.call { inherit ref; };
 
   tnpair = { tumour = {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};};
@@ -26,6 +28,13 @@ let
       mkdir $out/alignments
       ln -s ${tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.bam
       ln -s ${tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.bam
+      ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat
+      ln -s ${flagstat tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.flagstat
+      mkdir $out/fastqc
+      ln -s ${check tnpair.tumour.files.input1} $out/fastqc/${tnpair.tumour.name}.1
+      ln -s ${check tnpair.tumour.files.input2} $out/fastqc/${tnpair.tumour.name}.2
+      ln -s ${check tnpair.normal.files.input1} $out/fastqc/${tnpair.normal.name}.1
+      ln -s ${check tnpair.normal.files.input2} $out/fastqc/${tnpair.normal.name}.2
     '';
   };