diff options
| -rw-r--r-- | test-tnpair.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-variants.nix | 10 | ||||
| -rw-r--r-- | tools/gridss.nix | 6 |
3 files changed, 17 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index da37068..c88b68a 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -51,6 +51,7 @@ let (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss") (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2") + (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3") (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam") (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram") #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram") diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index b564725..4f39b1e 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -111,4 +111,14 @@ rec { gridss.assembly = assembly; }; }; + + annotateAndAssemble = stage rec { + name = "gridss-annotateVariants-assemble"; + buildCommand = '' + mkdir $out + ln -s ${annotate} $out/gridss.vcf + ln -s ${assembly} $out/gridss.bam + ln -s ${bionix.samtools.index indexAttrs assembly} $out/gridss.bam.bai + ''; + }; } diff --git a/tools/gridss.nix b/tools/gridss.nix index 050a628..176bd34 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -53,6 +53,9 @@ rec { */ annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate); + /* As annotateVariants except include assembly in output */ + annotateAndAssemble = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble); + /* Preprocess BAM files to extract SV reads and convert soft clips to split reads Type: preprocessBam :: bam -> bam */ @@ -69,4 +72,7 @@ rec { Type: [bam] -> GRIDSS result */ call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs); + + /* As call but include assemblies in output */ + callAndAssemble = inputs: gridss.annotateAndAssemble {} (map gridss.preprocessBam inputs); } |