From 95c8a36a7e673fac090175729069a668daa919da Mon Sep 17 00:00:00 2001
From: l-d-s <l@sdf.org>
Date: Wed, 1 May 2019 14:04:54 +1000
Subject: Add fastp.

---
 test-tnpair.nix | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

(limited to 'test-tnpair.nix')

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 1d281fa..1b5f347 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -14,7 +14,8 @@ let
   alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = samtools.sort {};
   flagstat = samtools.flagstat {};
-  check = fastqc.check {};
+  check-fastqc = fastqc.check {};
+  check-fastp = fastp.run {};
   callVariants = strelka.callSomatic {};
   markdup = samtools.markdup {};
   fixmate = samtools.fixmate {};
@@ -59,10 +60,11 @@ let
     #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram")
     (ln (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat")
     #(ln (flagstat tnpairResult.alignments.normal) "alignments/${tnpair.normal.name}.flagstat")
-    (ln (check tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1")
-    #(ln (check tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2")
-    #(ln (check tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1")
-    #(ln (check tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2")
+    (ln (check-fastqc tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1")
+    #(ln (check-fastqc tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1")
+    #(ln (check-fastqc tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2")
+    #(ln (check-fastqc tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2")
+    (ln (check-fastp tnpair.tumour.files) "fastp/${tnpair.tumour.name}")
   ];
 
 in testNaming
-- 
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