diff options
| author | Justin Bedo <cu@cua0.org> | 2021-02-19 11:18:10 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2021-02-19 11:18:10 +1100 |
| commit | 64f8b0cb124445620b30e10e268fd7670ccb3189 (patch) | |
| tree | 8aba918a125ad0c780bf8ccb4c0e41b2ab91a7f9 | |
| parent | 834d736a00f5bd7155cb137d5a3e94e1413e8ada (diff) | |
samtools-index: support cram indexing
| -rw-r--r-- | test-tnpair.nix | 1 | ||||
| -rw-r--r-- | tools/samtools-index.nix | 11 |
2 files changed, 8 insertions, 4 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 70fb5c8..7cc5453 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -64,6 +64,7 @@ let }; testNaming = linkOutputs { + crai = samtools.index {} (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour); kallisto = kallisto.quant {inherit ref;} (attrValues tnpair.tumour.files); facets = facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}; cnvkit = cnvkitResults.cnvs; diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix index d0f8d7a..62ee4c9 100644 --- a/tools/samtools-index.nix +++ b/tools/samtools-index.nix @@ -8,16 +8,19 @@ with bionix; with lib; with types; -assert (matchFiletype "samtools-index" { bam = _: true; } input); +assert (matchFiletype "samtools-index" { bam = _: true; cram = _: true; } input); assert (matchFileSorting "samtools-index" { coord = _: true; } input); +let + ext = matchFiletype "samtools-index-ext" { bam = _: "bam"; cram = _: "cram"; }; +in + stage { name = "samtools-index"; buildInputs = with pkgs; [ samtools ]; buildCommand = '' - ln -s ${input} input.bam - samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.bam - cp input.bam.bai $out + ln -s ${input} input.${ext input} + samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.${ext input} $out ''; passthru.multicore = true; } |