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| author | Justin Bedo <cu@cua0.org> | 2018-11-22 10:44:31 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-11-22 10:44:31 +1100 |
| commit | 0ade062d2da8a7111b14aa3d72ef7c741e98352d (patch) | |
| tree | 850a422cc3bcb72a414f3993e45bebcebbcc2565 /tools/gridss-identifyVariants.nix | |
| parent | 98e79735080b379e9a674a69771707951bbdc1ac (diff) | |
gridss: restructure gridss pipeline
Diffstat (limited to 'tools/gridss-identifyVariants.nix')
| -rw-r--r-- | tools/gridss-identifyVariants.nix | 12 |
1 files changed, 11 insertions, 1 deletions
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix index c91de00..d37e7ae 100644 --- a/tools/gridss-identifyVariants.nix +++ b/tools/gridss-identifyVariants.nix @@ -2,8 +2,8 @@ , nixpkgs , bwaIndexAttrs ? {} , faidxAttrs ? {} +, indexAttrs ? {} , assemblyAttrs ? {} -, extractSVReadsAttrs ? {} , collectMetricsAttrs ? {} , softClipsToSplitReadsAttrs ? {} , flags ? null @@ -34,6 +34,16 @@ let done ''; + linkSV = input: '' + BASENAME=$(basename ${input}) + WRKDIR="''${BASENAME}.gridss.working" + if [[ ! -e $WRKDIR ]] ; then + mkdir $WRKDIR + fi + ln -s ${input} $WRKDIR/$BASENAME.sv.bam + ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai + ''; + assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.samtools.sort { nameSort = true;} (bionix.gridss.assemble assemblyAttrs inputs))); in |