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(-) (limited to 'tools') 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(-) (limited to 'tools') 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 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(-) (limited to 'tools') 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