diff options
Diffstat (limited to 'tools/gridss-assemble.nix')
| -rw-r--r-- | tools/gridss-assemble.nix | 7 |
1 files changed, 3 insertions, 4 deletions
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index 1e25731..d1a3e4b 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -2,8 +2,8 @@ , nixpkgs , bwaIndexAttrs ? {} , faidxAttrs ? {} +, indexAttrs ? {} , collectMetricsAttrs ? {} -, extractSVReadsAttrs ? {} , flags ? null }: @@ -23,9 +23,8 @@ let BASENAME=$(basename ${input}) WRKDIR="''${BASENAME}.gridss.working" mkdir $WRKDIR - for f in ${bionix.gridss.extractSVReads extractSVReadsAttrs input}/* ; do - ln -s $f $WRKDIR/$BASENAME.''${f#*.} - done + ln -s ${input} $WRKDIR/$BASENAME.sv.bam + ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai for f in ${bionix.gridss.collectMetrics collectMetricsAttrs input}/* ; do ln -s $f $WRKDIR/$BASENAME.''${f#*.} done |