aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorJustin Bedo <cu@cua0.org>2019-05-21 18:23:02 +1000
committerJustin Bedo <cu@cua0.org>2019-05-21 18:23:47 +1000
commitb714521422af63a910ff660dcc019cbaeb6a5d17 (patch)
tree8d621e0b67b5e2efdd1eb19c2fb9e6951c2fc120
parent7b7f7c5eddfb3829cef8df7bf217d8309507cf2d (diff)
fastp: input filetypes
-rw-r--r--tools/fastp-check.nix10
1 files changed, 5 insertions, 5 deletions
diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix
index be807d6..bd522d8 100644
--- a/tools/fastp-check.nix
+++ b/tools/fastp-check.nix
@@ -7,12 +7,12 @@
} :
with bionix;
-with pkgs.lib;
+with lib;
with types;
-# Match input file type—how to do .fq and .fq.gz? Does bz2 work?
-
let
+ fq = f: matchFiletype "fastp-input" { fq = _: f; gz = matchFiletype' "fastp-input" { fq = _: f; }; } f;
+
out =
stage {
name = "fastp";
@@ -22,10 +22,10 @@ let
mkdir -p $out
fastp \
${optionalString (flags != null) flags} \
- -i ${input1} \
+ -i ${fq input1} \
-o fastq1.fq.gz \
${optionalString (input2 != null) ''
- -I ${input2} \
+ -I ${fq input2} \
-O fastq2.fq.gz \
cp fastq2.fq.gz $fastq2