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authorJustin Bedo <cu@cua0.org>2020-03-27 10:59:44 +1100
committerJustin Bedo <cu@cua0.org>2020-03-27 10:59:44 +1100
commitd4fe5ce2aaea3f951fe21094ccfa90360c12c760 (patch)
tree7a13fa9590fa70271c4da465ae02b6bca1e1879e
parent7a80f94a3aa69072e25b92098a746778707cb7d6 (diff)
update exampes to use nixpkgs.lib.pipe
-rw-r--r--examples/call.nix3
-rw-r--r--examples/ex-nextflow/nextflow-example1.nix4
-rw-r--r--examples/ex-tnpair/tnpair.nix2
3 files changed, 5 insertions, 4 deletions
diff --git a/examples/call.nix b/examples/call.nix
index 0e4ea05..90832ee 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -7,9 +7,10 @@
,ref ? bionix.ref.grch38.seq }:
with bionix;
+with lib;
let
- preprocess = pipe [
+ preprocess = flip pipe [
(bwa.align { inherit ref; })
(samtools.fixmate {})
(samtools.sort {})
diff --git a/examples/ex-nextflow/nextflow-example1.nix b/examples/ex-nextflow/nextflow-example1.nix
index 0ec1cae..4f00431 100644
--- a/examples/ex-nextflow/nextflow-example1.nix
+++ b/examples/ex-nextflow/nextflow-example1.nix
@@ -24,7 +24,7 @@ let
'';
};
-in pipe [
+in pipe input [
splitSequences
(each reverse)
-] input
+]
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index ada96c8..51cd703 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -11,7 +11,7 @@ with lib;
let
input = mapAttrs (_: fetchFastQGZ);
- preprocess = pipe [
+ preprocess = flip pipe [
input
(bwa.align { ref = fetchFastA ref; })
(samtools.fixmate {})