<commit_before># the output directory is a convention used in many workflows to specify a relative output path
output_dir=seqware-results
# the output_prefix is a convention used to specify the root of the absolute output path or an S3 bucket name
# you should pick a path that is available on all cluster nodes and can be written by your user
output_prefix=./
# cleanup true will remove just the input BAMs if not uploading and the full output directory if uploading
# false there will be no cleanup which is useful for debugging
cleanup=false

# START NEW ITEMS

# these are just used for tracking
donor_id=unknown
project_code=unknown

# tracking instance types
vm_instance_type=unknown
vm_instance_cores=unknown
vm_instance_mem_gb=unknown
vm_location_code=unknown

# cleanup
cleanupBams=false

# archive tarball
saveUploadArchive=true
uploadArchivePath=./seqware-results/upload_archive/

# options for tarball to SFTP
SFTPUploadArchive=true
# can be overwrite or skip, see https://trac.cyberduck.io/wiki/help/en/howto/cli
SFTPUploadArchiveMode=overwrite
SFTPUploadArchiveUsername=boconnor
SFTPUploadArchivePassword=<PASSWORD>
SFTPUploadArchiveServer=10.1.1.13
SFTPUploadArchivePath=/upload/path/directory/

# options for tarball to S3
S3UploadArchive=true
S3UploadArchiveMode=overwrite
S3UploadArchiveBucketURL=s3://bucketname/uploads/
S3UploadArchiveKey=<KEY>
S3UploadArchiveSecretKey=<KEY>

# send the files not a tarball
SFTPUploadFiles=true
# can be overwrite or skip, see https://trac.cyberduck.io/wiki/help/en/howto/cli
SFTPUploadMode=overwrite
SFTPUploadUsername=boconnor
SFTPUploadPassword=<PASSWORD>
SFTPUploadServer=10.1.1.13
SFTPUploadPath=/upload/path/directory/

S3UploadFiles=true
S3UploadFileMode=overwrite
S3UploadBucketURL=s3://bucketname/uploads/
S3UploadKey=<KEY>
S3UploadSecretKey=<KEY>

# synapse upload
SynapseUpload=true
SynapseUploadSFTPUsername=boconnor
SynapseUploadSFTPPassword=<PASSWORD>
SynapseUploadUsername=boconnor
SynapseUploadPassword=<PASSWORD>
SynapseUploadURL=sftp://tcgaftps.nci.nih.gov/tcgapancan/pancan/variant_calling_pilot_64/OICR_Sanger_Core
SynapseUploadParent=syn3155834

# if set, these trigger an upload of the input bam file to a GNOS repository
bamUploadServer=
bamUploadPemFile=
bamUploadStudyRefnameOverride=
bamUploadAnalysisCenterOverride=
bamUploadScriptJobMem=10000
bamUploadScriptJobSlots=1

# if set to true GNOS is still used for downloading metadata but the input bam file paths are assumed to be local file paths
# specifically tumourBams is a colon-delimited list of full file paths and controlBam is a full file path
localFileMode=false

# END NEW ITEMS

# basic setup
coresAddressable=32
memHostMbAvailable=240000
tabixSrvUri=http://10.89.9.50/

# Use public pulldown data bundled with workflow instead of full genome scale data from GNOS
#testMode=true

pemFile=/mnt/seqware-build/ebi.pem
gnosServer=https://gtrepo-ebi.annailabs.com
## comment out upload server to block vcfUpload
uploadServer=https://gtrepo-ebi.annailabs.com
uploadPemFile=/mnt/seqware-build/ebi.pem

study-refname-override=icgc_pancancer_vcf_test
#analysis-center-override=
#center-override=
#ref-center-override=
#upload-test=true
#upload-skip=true

assembly=GRCh37
species=human
seqType=WGS
gender=L

# PD13491a 36x tumour, other test data, GNOS download
#tumourAliquotIds=f86b6ba2-8f4b-ee53-e040-11ac0d485904
#tumourAnalysisIds=0772aed3-4df7-403f-802a-808df2935cd1
#tumourBams=c007f362d965b32174ec030825262714.bam
# PD13491b 30x normal
#controlAnalysisId=5161b68b-e757-47df-80cf-79554430e5cb
#controlBam=459793d5b324900a2f9dd1ec079a368e.bam

# PD4116a 30x vs PD4116b 30x
tumourAliquotIds=f393bb07-270c-2c93-e040-11ac0d484533
tumourAnalysisIds=ef26d046-e88a-4f21-a232-16ccb43637f2
tumourBams=7723a85b59ebce340fe43fc1df504b35.bam
controlAnalysisId=1b9215ab-3634-4108-9db7-7e63139ef7e9
controlBam=8f957ddae66343269cb9b854c02eee2f.bam

refExclude=MT,GL%,hs37d5,NC_007605

# GENOS
memBasFileGet=4000
memGnosDownload=15000
memUpload=5000

# GENERIC
memWorkflowOverhead=3000
memPackageResults=4000
memMarkTime=4000
memGenotype=4000
memContam=4000
memQcMetrics=4000
memGetTbi=4000

contamDownSampOneIn=25

#PICNIC
memPicnicCounts=4000
memPicnicMerge=4000

#BATTENBERG
memUnpack=4000
memBbMerge=4000

# ASCAT
memAlleleCount=4000
memAscat=8000
memAscatFinalise=4000

# PINDEL
memPindelInput=12000
memPindelPerThread=8000
memPindelVcf=8000
memPindelMerge=6000
memPindelFlag=8000

# BRASS
memBrassInput=6000
memBrassGroup=4500
memBrassFilter=4500
memBrassSplit=4000
memBrassAssemblePerThread=4000
memBrassGrass=4000
memBrassTabix=4000

# CAVEMAN
memCaveCnPrep=4000
memCavemanSetup=4000
memCavemanSplit=4000
memCavemanSplitConcat=4000
memCavemanMstepPerThread=3000
memCavemanMerge=4000
memCavemanEstepPerThread=3000
memCavemanMergeResults=4000
memCavemanAddIds=4000
memCavemanFlag=5000
memCavemanTbiClean=4000
<commit_msg>Update the mem for gnos<commit_after># the output directory is a convention used in many workflows to specify a relative output path
output_dir=seqware-results
# the output_prefix is a convention used to specify the root of the absolute output path or an S3 bucket name
# you should pick a path that is available on all cluster nodes and can be written by your user
output_prefix=./
# cleanup true will remove just the input BAMs if not uploading and the full output directory if uploading
# false there will be no cleanup which is useful for debugging
cleanup=false

# START NEW ITEMS

# these are just used for tracking
donor_id=unknown
project_code=unknown

# tracking instance types
vm_instance_type=unknown
vm_instance_cores=unknown
vm_instance_mem_gb=unknown
vm_location_code=unknown

# cleanup
cleanupBams=false

# archive tarball
saveUploadArchive=true
uploadArchivePath=./seqware-results/upload_archive/

# options for tarball to SFTP
SFTPUploadArchive=true
# can be overwrite or skip, see https://trac.cyberduck.io/wiki/help/en/howto/cli
SFTPUploadArchiveMode=overwrite
SFTPUploadArchiveUsername=boconnor
SFTPUploadArchivePassword=<PASSWORD>
SFTPUploadArchiveServer=10.1.1.13
SFTPUploadArchivePath=/upload/path/directory/

# options for tarball to S3
S3UploadArchive=true
S3UploadArchiveMode=overwrite
S3UploadArchiveBucketURL=s3://bucketname/uploads/
S3UploadArchiveKey=<KEY>
S3UploadArchiveSecretKey=<KEY>

# send the files not a tarball
SFTPUploadFiles=true
# can be overwrite or skip, see https://trac.cyberduck.io/wiki/help/en/howto/cli
SFTPUploadMode=overwrite
SFTPUploadUsername=boconnor
SFTPUploadPassword=<PASSWORD>
SFTPUploadServer=10.1.1.13
SFTPUploadPath=/upload/path/directory/

S3UploadFiles=true
S3UploadFileMode=overwrite
S3UploadBucketURL=s3://bucketname/uploads/
S3UploadKey=<KEY>
S3UploadSecretKey=<KEY>

# synapse upload
SynapseUpload=true
SynapseUploadSFTPUsername=boconnor
SynapseUploadSFTPPassword=<PASSWORD>
SynapseUploadUsername=boconnor
SynapseUploadPassword=<PASSWORD>
SynapseUploadURL=sftp://tcgaftps.nci.nih.gov/tcgapancan/pancan/variant_calling_pilot_64/OICR_Sanger_Core
SynapseUploadParent=syn3155834

# if set, these trigger an upload of the input bam file to a GNOS repository
bamUploadServer=
bamUploadPemFile=
bamUploadStudyRefnameOverride=
bamUploadAnalysisCenterOverride=
bamUploadScriptJobMem=10000
bamUploadScriptJobSlots=1

# if set to true GNOS is still used for downloading metadata but the input bam file paths are assumed to be local file paths
# specifically tumourBams is a colon-delimited list of full file paths and controlBam is a full file path
localFileMode=false

# END NEW ITEMS

# basic setup
coresAddressable=32
memHostMbAvailable=240000
tabixSrvUri=http://10.89.9.50/

# Use public pulldown data bundled with workflow instead of full genome scale data from GNOS
#testMode=true

pemFile=/mnt/seqware-build/ebi.pem
gnosServer=https://gtrepo-ebi.annailabs.com
## comment out upload server to block vcfUpload
uploadServer=https://gtrepo-ebi.annailabs.com
uploadPemFile=/mnt/seqware-build/ebi.pem

study-refname-override=icgc_pancancer_vcf_test
#analysis-center-override=
#center-override=
#ref-center-override=
#upload-test=true
#upload-skip=true

assembly=GRCh37
species=human
seqType=WGS
gender=L

# PD13491a 36x tumour, other test data, GNOS download
#tumourAliquotIds=f86b6ba2-8f4b-ee53-e040-11ac0d485904
#tumourAnalysisIds=0772aed3-4df7-403f-802a-808df2935cd1
#tumourBams=c007f362d965b32174ec030825262714.bam
# PD13491b 30x normal
#controlAnalysisId=5161b68b-e757-47df-80cf-79554430e5cb
#controlBam=459793d5b324900a2f9dd1ec079a368e.bam

# PD4116a 30x vs PD4116b 30x
tumourAliquotIds=f393bb07-270c-2c93-e040-11ac0d484533
tumourAnalysisIds=ef26d046-e88a-4f21-a232-16ccb43637f2
tumourBams=7723a85b59ebce340fe43fc1df504b35.bam
controlAnalysisId=1b9215ab-3634-4108-9db7-7e63139ef7e9
controlBam=8f957ddae66343269cb9b854c02eee2f.bam

refExclude=MT,GL%,hs37d5,NC_007605

# GENOS
memBasFileGet=4000
memGnosDownload=14000
memUpload=14000

# GENERIC
memWorkflowOverhead=3000
memPackageResults=4000
memMarkTime=4000
memGenotype=4000
memContam=4000
memQcMetrics=4000
memGetTbi=4000

contamDownSampOneIn=25

#PICNIC
memPicnicCounts=4000
memPicnicMerge=4000

#BATTENBERG
memUnpack=4000
memBbMerge=4000

# ASCAT
memAlleleCount=4000
memAscat=8000
memAscatFinalise=4000

# PINDEL
memPindelInput=12000
memPindelPerThread=8000
memPindelVcf=8000
memPindelMerge=6000
memPindelFlag=8000

# BRASS
memBrassInput=6000
memBrassGroup=4500
memBrassFilter=4500
memBrassSplit=4000
memBrassAssemblePerThread=4000
memBrassGrass=4000
memBrassTabix=4000

# CAVEMAN
memCaveCnPrep=4000
memCavemanSetup=4000
memCavemanSplit=4000
memCavemanSplitConcat=4000
memCavemanMstepPerThread=3000
memCavemanMerge=4000
memCavemanEstepPerThread=3000
memCavemanMergeResults=4000
memCavemanAddIds=4000
memCavemanFlag=5000
memCavemanTbiClean=4000

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