diff options
author | l-d-s <distefano.l@wehi.edu.au> | 2018-11-22 12:04:23 +1100 |
---|---|---|
committer | l-d-s <distefano.l@wehi.edu.au> | 2018-11-22 12:04:23 +1100 |
commit | 7c36ee4ec628767c834ad803aac76d93e31f0486 (patch) | |
tree | 2edf423614fc077c4027b7996f690b004ec4f25b /tools/gridss-assemble.nix | |
parent | 3c568bacd397a3ddcb203811f7fa5a1f8af760a3 (diff) | |
parent | 0ade062d2da8a7111b14aa3d72ef7c741e98352d (diff) |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
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 |