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| author | Justin Bedo <cu@cua0.org> | 2020-09-02 16:24:37 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2020-09-02 16:24:37 +1000 |
| commit | 9cf1724895f001c625fba37d78f517acb6938e07 (patch) | |
| tree | cef3900c0ffd13a3e71763d38bd85d893a3ce3ec /tools/gridss-assemble.nix | |
| parent | f3dc7987e0e841b97fd43160c68f8d09265083bc (diff) | |
gridss: shard assembly into 10 pieces by default
Diffstat (limited to 'tools/gridss-assemble.nix')
| -rw-r--r-- | tools/gridss-assemble.nix | 15 |
1 files changed, 13 insertions, 2 deletions
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index a532f4b..f0a2693 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -6,6 +6,9 @@ , flags ? null , config ? null , heapSize ? "31g" +, workdirs ? [] +, jobIndex ? null +, jobNodes ? null }: with bionix; @@ -37,7 +40,8 @@ assert (homoRef); stage rec { name = "gridss-assemble"; - buildInputs = with pkgs; [ jre bwa ]; + buildInputs = with pkgs; [ jre bwa rsync ]; + outputs = [ "out" "work" ]; buildCommand = '' TMPDIR=$(pwd) ln -s ${ref} ref.fa @@ -46,7 +50,8 @@ stage rec { ln -s $f done ${concatMapStringsSep "\n" linkInput inputs} - java -Xmx${heapSize} -Dsamjdk.create_index=true \ + ${concatMapStringsSep "\n" (w: "rsync -a --ignore-existing ${w}/ ./") workdirs} + java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${bionix.gridss.jar} gridss.AssembleBreakends \ VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ @@ -56,7 +61,13 @@ stage rec { ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ \ + ${optionalString (jobIndex != null) "JOB_INDEX=${toString jobIndex}"} \ + ${optionalString (jobIndex != null) "JOB_NODES=${toString jobNodes}"} \ ${optionalString (flags != null) flags} + rm -rf tmp + touch $out + cp -r $TMPDIR $work + chmod u+rwX -R $work ''; passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; }; passthru.multicore = true; |