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| author | Justin Bedo <cu@cua0.org> | 2019-04-30 13:05:17 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-04-30 13:05:17 +1000 |
| commit | d517a934f570427e46be8d83aa2ae4b045b069e8 (patch) | |
| tree | f419839a9405b0e252f0e7753623fe2c52c5d447 /examples/ex-tnpair | |
| parent | 5d03ab8afa1803ddabc7616a48fff9889e3a0c51 (diff) | |
Add examples and example README
Diffstat (limited to 'examples/ex-tnpair')
| -rwxr-xr-x | examples/ex-tnpair/tnpair | 2 | ||||
| -rw-r--r-- | examples/ex-tnpair/tnpair.nix | 4 |
2 files changed, 3 insertions, 3 deletions
diff --git a/examples/ex-tnpair/tnpair b/examples/ex-tnpair/tnpair index 5b84d5c..d90374b 100755 --- a/examples/ex-tnpair/tnpair +++ b/examples/ex-tnpair/tnpair @@ -55,4 +55,4 @@ import ./tnpair.nix { } EOF -nix build --keep-going "(import ./tnpair-$$)" +nix build --keep-going "(import ./tnpair-$$)" --no-sandbox diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix index 2939db4..c42fe95 100644 --- a/examples/ex-tnpair/tnpair.nix +++ b/examples/ex-tnpair/tnpair.nix @@ -1,5 +1,5 @@ # This is an example tumour-normal calling pipeline using strelka -{ bionix ? import <bionix> {} +{ bionix ? import ./../.. {} , normal , tumour , ref @@ -20,7 +20,7 @@ let ]; in linkDrv [ - (ln (strelka.call {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka") + (ln (strelka.callSomatic {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka") (ln (preprocess normal) "normal.bam") (ln (preprocess tumour) "tumour.bam") ] |