diff options
| author | l-d-s <l@sdf.org> | 2018-11-15 16:11:14 +1100 |
|---|---|---|
| committer | l-d-s <l@sdf.org> | 2018-11-15 16:11:14 +1100 |
| commit | 5ad075658eea3d783bac013aae476dd22a371e71 (patch) | |
| tree | d0b38bcdb4e3aeaabbcd99aee24bb8a40ea86f24 | |
| parent | dfb20e1741e8785fae8527c881954de33b7c72ac (diff) | |
| parent | c2da3532235bd45ddb1105600d4ba74a70dadeca (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
| -rwxr-xr-x | lib/references.nix | 22 | ||||
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 8 | ||||
| -rw-r--r-- | tools/gridss.nix | 4 |
3 files changed, 26 insertions, 8 deletions
diff --git a/lib/references.nix b/lib/references.nix index bdeefa6..1ac92de 100755 --- a/lib/references.nix +++ b/lib/references.nix @@ -82,6 +82,28 @@ rec { buildCommand = "gunzip < $src > $out"; passthru.filetype = filetype.fa {}; }; + ensembl = { + cdna = stdenvNoCC.mkDerivation rec { + name = "ensembl-grch38-cdna-${version}"; + version = "94"; + src = fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz"; + sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + ncrna = stdenvNoCC.mkDerivation rec { + name = "ensembl-grch38-ncrna-${version}"; + version = "94"; + src = fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz"; + sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + }; }; mm10 = mm10-p4; diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 35cd7b4..5fce894 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -21,7 +21,7 @@ assert (matchFileSorting "gridss-softClipsToSplitReads" { name = _: true; } inpu stdenv.mkDerivation rec { name = "gridss-softClipsToSplitReads"; - buildInputs = [ jre ]; + buildInputs = [ jre bwa ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai @@ -37,9 +37,5 @@ stdenv.mkDerivation rec { ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ WORKER_THREADS=$NIX_BUILD_CORES ''; - passthru.filetype = - if alignerStreaming then - filetype.bam { ref = ref; sort = sorting.none {}; } - else - input.filetype; + passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {}; } } diff --git a/tools/gridss.nix b/tools/gridss.nix index bc2f0b8..1e4e2d1 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -17,6 +17,6 @@ rec { assemble = callBionix ./gridss-assemble.nix; identifyVariants = callBionix ./gridss-identifyVariants.nix; annotateVariants = callBionix ./gridss-annotateVariants.nix; - preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (softClipsToSplitReads {} (computeSamTags {} (sort {nameSort = true;} input))))); - call = inputs: annotateVariants {} (map preprocessBam inputs); + preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (bionix.gridss.softClipsToSplitReads {} (bionix.gridss.computeSamTags {} (sort {nameSort = true;} input))))); + call = inputs: bionix.gridss.annotateVariants {} (map bionix.gridss.preprocessBam inputs); } |