From c45a6b1c1b68cd08efe55ec1df197c0c26b5ca49 Mon Sep 17 00:00:00 2001 From: l-d-s Date: Wed, 7 Nov 2018 10:03:20 +1100 Subject: Add bwa to softClipsToSplitReads --- tools/gridss-softClipsToSplitReads.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 8a7dca3..cc40e52 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -20,7 +20,7 @@ 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 -- cgit v1.2.3 From 886af7beaaa98ac32db88a7453d917409cf11ae8 Mon Sep 17 00:00:00 2001 From: l-d-s Date: Wed, 7 Nov 2018 16:39:47 +1100 Subject: Fix to gridss. --- tools/gridss.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/gridss.nix b/tools/gridss.nix index d46a8ce..792d279 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -16,6 +16,6 @@ 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); } -- cgit v1.2.3 From 08f9d475e616c1034bcb04b8ad9ac4f139b4be9e Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 14 Nov 2018 13:53:49 +1100 Subject: Add ensembl mouse transcriptome --- lib/references.nix | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) 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; -- cgit v1.2.3 From c2da3532235bd45ddb1105600d4ba74a70dadeca Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 15 Nov 2018 15:13:50 +1100 Subject: gridss.softClipsToSplitReads: sort ordering is not preserved NB: this breaks gridss.preprocessBam --- tools/gridss-softClipsToSplitReads.nix | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index b35d41d..5fce894 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -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 {}; } } -- cgit v1.2.3