Few more fixes

hartwigmedical · May 24, 2018 · c9c1498 · c9c1498
1 parent 60c7b0b
commit c9c1498
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Showing 2 changed files with 1 addition and 7 deletions.
diff --git a/settings/Somatic.ini b/settings/Somatic.ini
@@ -14,7 +14,7 @@ AMBER	yes
 COBALT	yes
 PURPLE	yes
 
-STRUCTURAL_VARIANT_CALLING	YES
+STRUCTURAL_VARIANT_CALLING	yes
 MANTA	yes
 
 HEALTHCHECK	yes

diff --git a/templates/Manta.sh.tt b/templates/Manta.sh.tt
@@ -7,19 +7,13 @@
 cd "[% opt.OUTPUT_DIR %]"
 
 assert_not_empty "[% sample_bam %]"
-[% IF opt.SV_MODE == "sample_control" %]
 assert_not_empty "[% control_bam %]"
 [% opt.MANTA_PATH %]/configManta.py --referenceFasta "[% opt.GENOME %]" --runDir "[% dirs.out %]" --normalBam "[% control_bam %]" --tumorBam "[% sample_bam %]" --generateEvidenceBam
-[% ELSE %]
-[% opt.MANTA_PATH %]/configManta.py --referenceFasta "[% opt.GENOME %]" --runDir "[% dirs.out %]" --bam "[% sample_bam %]"
-[% END %]
 
 [% dirs.out %]/runWorkflow.py -m local -j [% opt.MANTA_THREADS %]
 
 assert_not_empty "[% dirs.out %]/results/variants/diploidSV.vcf.gz.tbi"
-[%- IF opt.SV_MODE == "sample_control" %]
 assert_not_empty "[% dirs.out %]/results/variants/somaticSV.vcf.gz.tbi"
-[%- END %]
 
 [ "$(cat "[% dirs.out %]/workflow.exitcode.txt")" == "0" ] || failure "Manta workflow logged non-zero exit code."