Merge pull request #87 from CuppenResearch/develop

Release v2.4.1

Author: rernst

settings/CPCT.ini

@@ -311,4 +311,4 @@ CHECKING_QUEUE	all.q
 CHECKING_TIME	24:0:0
 CHECKING_THREADS	1
 CHECKING_MEM	10
-CHECKING_RM	tmp,*.pileup.gz,*.pileup.gz.tbi
+CHECKING_RM	tmp,*.pileup.gz,*.pileup.gz.tbi,*.recalibrated.bam,*.recalibrated.bai,*.recalibrated.bam.bai

settings/UMCU_Genome_somatic.ini

@@ -312,4 +312,4 @@ CHECKING_QUEUE	all.q
 CHECKING_TIME	24:0:0
 CHECKING_THREADS	1
 CHECKING_MEM	10
-CHECKING_RM	tmp,*.pileup.gz,*.pileup.gz.tbi
+CHECKING_RM	tmp,*.pileup.gz,*.pileup.gz.tbi,*.recalibrated.bam,*.recalibrated.bai,*.recalibrated.bam.bai

settings/UMCU_MIPS.ini

@@ -157,4 +157,4 @@ CHECKING_QUEUE	all.q
 CHECKING_TIME	2:0:0
 CHECKING_THREADS	1
 CHECKING_MEM	10
-CHECKING_RM	tmp,*.pileup.gz,*.pileup.gz.tbi
+CHECKING_RM	tmp

settings/dummy.conf

@@ -21,4 +21,4 @@ BAM	/hpc/cog_bioinf/data/robert/testIAP/testData/bams/CONTROLP26.bam
 BAM	/hpc/cog_bioinf/data/robert/testIAP/testData/bams/CONTROLP27.bam
 
 ### OR VCF FILE ###
-VCF	/hpc/cog_bioinf/data/robert/testIAP/testData/vcf/testCreatConfig.raw_variants.vcf
+VCF	/hpc/cog_bioinf/data/robert/testIAP/testData/vcf/testCreatConfig.raw_variants.vcf

settings/hartwig_kg.ini

@@ -7,7 +7,7 @@
 CLUSTER_PATH	/opt/sge/default/common
 CLUSTER_TMP	/tmp
 CLUSTER_RESERVATION	yes
-CLUSTER_PROJECT	cog_bioinf
+CLUSTER_PROJECT	diaggen
 
 ####TOOL PATHS####
 # Mapping
@@ -354,4 +354,4 @@ CHECKING_QUEUE	all.q
 CHECKING_TIME	24:0:0
 CHECKING_THREADS	1
 CHECKING_MEM	10
-CHECKING_RM	tmp
+CHECKING_RM	tmp,*.recalibrated.bam,*.recalibrated.bai,*.recalibrated.bam.bai

settings/illumina_pipeline.ini.dummy

@@ -345,4 +345,4 @@ NIPT_THREADS	4
 CHECKING_QUEUE	all.q
 CHECKING_TIME	2:0:0
 CHECKING_THREADS	1
-CHECKING_RM	tmp,*.pileup.gz,*.pileup.gz.tbi
+CHECKING_RM	tmp,*.recalibrated.bam,*.recalibrated.bai,*.recalibrated.bam.bai