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author | l-d-s <distefano.l@wehi.edu.au> | 2018-12-12 10:30:27 +1100 |
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committer | l-d-s <distefano.l@wehi.edu.au> | 2018-12-12 10:30:27 +1100 |
commit | 875d5f28926a2dd3e066a4ce08a2ce18baee4661 (patch) | |
tree | f76116cd6b1a915ece6b1e2435745a420d9eee5a /tools/gridss-annotateVariants.nix | |
parent | f0357e09b8c473b55d22c4632692fcc79021570d (diff) | |
parent | 979bf4c65ad668b668750b58eefa9996f51b1242 (diff) |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools/gridss-annotateVariants.nix')
-rw-r--r-- | tools/gridss-annotateVariants.nix | 88 |
1 files changed, 0 insertions, 88 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix deleted file mode 100644 index e0a6f0f..0000000 --- a/tools/gridss-annotateVariants.nix +++ /dev/null @@ -1,88 +0,0 @@ -{ bionix -, nixpkgs -, bwaIndexAttrs ? {} -, faidxAttrs ? {} -, indexAttrs ? {} -, assemblyAttrs ? {} -, collectMetricsAttrs ? {} -, softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } -, identifyVariantsAttrs ? {} -, flags ? null -, config ? null -, heapSize ? "4g" - -}: - -with nixpkgs; -with lib; -with bionix.types; -with bionix.gridss; - -inputs: - -let - getref = matchFiletype "gridss-annotateVariants" { bam = x: x.ref; }; - ref = getref (head inputs); - sorted = matchFileSorting "gridss-annotateVariants" { coord = _: true; }; - homoRef = length (unique (map getref inputs)) == 1; - - linkInput = f: attrs: input: '' - BASENAME=$(basename ${input}) - WRKDIR="''${BASENAME}.gridss.working" - if [[ ! -e $WRKDIR ]] ; then - mkdir $WRKDIR - fi - for f in ${f attrs input}/* ; do - ln -s $f $WRKDIR/$BASENAME.''${f##*.} - done - ''; - - linkSV = input: '' - BASENAME=$(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.gridss.assemble assemblyAttrs inputs)); -in - -assert (all sorted inputs); -assert (homoRef); - -stdenv.mkDerivation rec { - name = "gridss-identifyVariants"; - buildInputs = [ jre ]; - buildCommand = '' - TMPDIR=$(pwd) - ln -s ${ref} ref.fa - ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai - for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do - ln -s $f - done - ${concatMapStringsSep "\n" (linkSV) inputs} - ${linkSV assembly} - ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs} - ${linkInput collectMetrics collectMetricsAttrs assembly} - ln -s ${identifyVariants identifyVariantsAttrs inputs} input.vcf - java -Xmx${heapSize} -Dsamjdk.create_index=true \ - -cp ${jar} gridss.AnnotateVariants \ - REFERENCE_SEQUENCE=ref.fa \ - ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ - ASSEMBLY=${assembly} \ - INPUT_VCF=input.vcf \ - OUTPUT_VCF=out.vcf \ - WORKING_DIR=$TMPDIR/ \ - ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ - TMP_DIR=$TMPDIR/ - - mv out.vcf $out - ''; - passthru = { - filetype = filetype.vcf { ref = ref; }; - gridss.assembly = assembly; - }; -} |