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| author | Justin Bedo <cu@cua0.org> | 2020-03-27 10:59:44 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2020-03-27 10:59:44 +1100 |
| commit | d4fe5ce2aaea3f951fe21094ccfa90360c12c760 (patch) | |
| tree | 7a13fa9590fa70271c4da465ae02b6bca1e1879e | |
| parent | 7a80f94a3aa69072e25b92098a746778707cb7d6 (diff) | |
update exampes to use nixpkgs.lib.pipe
| -rw-r--r-- | examples/call.nix | 3 | ||||
| -rw-r--r-- | examples/ex-nextflow/nextflow-example1.nix | 4 | ||||
| -rw-r--r-- | examples/ex-tnpair/tnpair.nix | 2 |
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 {}) |