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-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