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sisyphus.yml
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sisyphus.yml
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# Example YAML-file for sisyphus configuration
# Address for quick report
MAIL: [email protected]
# Sender address for quick report
SENDER: [email protected]
# CASAVA binaries
CASAVA: /opt/CASAVA/1.8.4/bin/
#Path to bcl2fastq binaries
BCL2FASTQ: /usr/local/bin/bcl2fastq-v2.17.1.14
# Demultiplex mismatches, set to 1 or 0 for each index read individually
# Default is to allow one mismatch in all index reads
MISMATCH:
1: 1
2: 1
MACHINES:
D00457:
TYPE: hiseq
D00118:
TYPE: hiseq
D00458:
TYPE: hiseq
M00485:
TYPE: miseq
M06455:
TYPE: miseq
SN7001335:
TYPE: hiseq
SN866:
TYPE: hiseq
ST-E00215:
TYPE: hiseqx
ST-E00216:
TYPE: hiseqx
ST-E00274:
TYPE: hiseqx
ST-E00279:
TYPE: hiseqx
ST-E00280:
TYPE: hiseqx
# The host on which to upload runfolder and execute sbatch jobs
REMOTE_HOST: milou-b.uppmax.uu.se
# The directory on REMOTE_HOST to put the runfolder in
REMOTE_PATH: /proj/a2009002/private/nobackup/runfolders
# Array with extra perl library paths
# This is where non system default libraries which are not
# included with sisyphus should be installed
# Currently, the only required extra module on Uppmax Milou is
# PDL (http://pdl.perl.org/) and its dependencies
PERL5LIB:
- /proj/a2009002/perl/lib/perl5/
# The directory on REMOTE_HOST to put the data for delivery in
OUTBOX_PATH: DEFAULT
# The host path to where data that should be processed with NGI-pipeline will be delivered.
NGI_HOST: nestor.uppmax.uu.se
# The port on which the ngi pipeline will respond on the remote host.
NGI_PORT: 6666
# The host path where NGI-pipeline data should be delivered.
NGI_REMOTE_PATH: /proj/a2015179/archive/
# The project that should have access to the data.
NGI_PROJECT: a2015179
# Change to 1 to process with NGI-pipeline
NGI_PROCESSING: 0
# Change to 1 to perform indeck check before demultiplexing
PRE_DEMULTIPLEX_INDEX_CHECK: 0
# Change to 1 to ignore missing fastqs
IGNORE_MISSING_FASTQS: 1
# Change to 0 to not use ssverify.sh for archive verification and instead use
# sisyphus own verfication procedure
USE_SSVERIFY: 1
# The host on which to archive the runfolder
ARCHIVE_HOST: milou-b.uppmax.uu.se
# The directory on ARCHIVE_HOST to put the runfolder in
# sisyphus will automatically add YYYY-MM to the path
# Default to nobackup dir as this will only be used while
# staging the data for transfer to Swestore
# This way we can hardlink instead of copy fastq-files
ARCHIVE_PATH: /proj/a2009002/private/nobackup/archive-tmp
# The iRODS path to SweStore archive
SWESTORE_PATH: /ssUppnexZone/proj/a2009002
# Root dir of temporary directory to use
# (eg when verifying the archive copies)
TEMP_PATH: /proj/a2009002/private/nobackup/tmp
# The host on which to put the summaries
SUMMARY_HOST: mm-xlas002
# The directory on ARCHIVE_HOST to put the runfolder in
SUMMARY_PATH: /mnt/Seq-Summaries/2016/
# The path, relative to the runfolder, where MiSeq analysis output is deposited
ANALYSIS_PATH: ../MiSeqAnalysis/
# The UPPNEX project to use for processing
UPPNEX_PROJECT: ngi2016001
# The UPPNEX project qos-flag to use for high priority processing
#UPPNEX_QOS: seqver
# The maximum error in a lane before filtering out bad tiles (%)
MAX_LANE_ERROR: 2
# The maximum error in a tile in a lane with too high error (%)
MAX_TILE_ERROR: 2
# Skip delivery of the following lanes
#SKIP_LANES:
# - 1
# - 2
# END