From 334bc692c821b1131744d1408ffe3a3ab71bf9cd Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 27 Feb 2020 12:55:44 +0100 Subject: [PATCH 1/2] fix bwa reference No idea if this is tested, but shouldn't BWA get an index in stead of a fasta reference? If this checks out, feel free to merge. If not, just close it again. Cheers M --- janis_bioinformatics/tools/bwa/mem/base.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/janis_bioinformatics/tools/bwa/mem/base.py b/janis_bioinformatics/tools/bwa/mem/base.py index 80e1c9d35..325954aa0 100644 --- a/janis_bioinformatics/tools/bwa/mem/base.py +++ b/janis_bioinformatics/tools/bwa/mem/base.py @@ -17,7 +17,7 @@ ToolMetadata, ) -from janis_bioinformatics.data_types import Sam, FastaWithDict, FastqGzPair +from janis_bioinformatics.data_types import Sam, bwaIndex, FastqGzPair from janis_bioinformatics.tools.bioinformaticstoolbase import BioinformaticsTool BWA_MEM_TUPLE = [ @@ -64,7 +64,7 @@ def base_command(self): def inputs(self): return [ - ToolInput("reference", FastaWithDict(), position=9), + ToolInput("reference", bwaIndex(), position=9), ToolInput("reads", FastqGzPair, position=10, doc=None), ToolInput("mates", FastqGzPair(optional=True), position=11, doc=None), ToolInput("outputFilename", Filename(extension=".sam")), From 7a959520ec266cc0fa05319455d061dba4a24d52 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 27 Feb 2020 13:08:04 +0100 Subject: [PATCH 2/2] fix FastaBwa reference --- janis_bioinformatics/tools/bwa/mem/base.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/janis_bioinformatics/tools/bwa/mem/base.py b/janis_bioinformatics/tools/bwa/mem/base.py index 325954aa0..449201ff9 100644 --- a/janis_bioinformatics/tools/bwa/mem/base.py +++ b/janis_bioinformatics/tools/bwa/mem/base.py @@ -17,7 +17,7 @@ ToolMetadata, ) -from janis_bioinformatics.data_types import Sam, bwaIndex, FastqGzPair +from janis_bioinformatics.data_types import Sam, FastaBwa, FastqGzPair from janis_bioinformatics.tools.bioinformaticstoolbase import BioinformaticsTool BWA_MEM_TUPLE = [ @@ -64,7 +64,7 @@ def base_command(self): def inputs(self): return [ - ToolInput("reference", bwaIndex(), position=9), + ToolInput("reference", FastaBwa(), position=9), ToolInput("reads", FastqGzPair, position=10, doc=None), ToolInput("mates", FastqGzPair(optional=True), position=11, doc=None), ToolInput("outputFilename", Filename(extension=".sam")),