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fgcz.conf
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fgcz.conf
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[ _ ]
# lab's name for the batch YAML description
lab=fgcz
# name of the _SFTP_ server, as used when fetching data files (i.e.: same name as in netrc file)
fileserver=fgcz-gstore.uzh.ch
# port used by SFTP, in case of non standard (you can also use ~/.ssh/config for that)
srvport=666
# experiment name in sftp store
#expname=/projects/p23212
expname=/projects
#projlist=( 'p23224' 'p23212' 'p24991' 'p25650' 'p26177' 'p30045' )
#Limit projects only to wastewater:
projlist=( 'p23224' 'p26177' 'p30045' 'p24991' )
# base dircetory (default: cwd)
basedir=/links/shared/covid19-pangolin/backup
# sub-directory to hold the unsorted downloaded datasets
download=bfabric-downloads
## sub-directory to hold the sorted samples set
#sampleset=staging-fcgz
sampleset=sampleset
# explicit list of orders spread among multiple batches that should be merged
fuselist=MS547_COV19_o23391,MS547_COV19_o23391_copy,NOV584_COV19_o23860,NOV593_COV19_o23860,NOV671_COV19_o24453,NOV671_COV19_o24453_copy,MiSeq_210820_MS639_o25795_DataDelivery_part,MiSeq_210820_MS640_o25795_DataDelivery_part,MiSeq_210820_MS639_o25796_part,MiSeq_210820_MS640_o25796_part,NovaSeq_20220708_NOV1343_o28874_DataDelivery,NovaSeq_20220715_NOV1355_o28874_DataDelivery
# delay after which orders aren't considered for merging anymore
fusedays=9
nofuselist=iSeq195_COV19_p23212_o25355,NOV816_COV19_p23212_o25355,NovaSeq_20210917_NOV929_o26053_DataDelivery,NovaSeq_20210917_NOV928_o26053_DataDelivery,NovaSeq_20210910_NOV920_o26053_DataDelivery,NovaSeq_20211119_NOV1039_o26703_DataDelivery,NovaSeq_20211119_NOV1039_o26712_DataDelivery,NovaSeq_20211122_NOV1041_o26703_DataDelivery,NovaSeq_20211122_NOV1041_o26712_DataDelivery,NovaSeq_20211220_NOV1084_copy_o27040_DataDelivery,NovaSeq_20211220_NOV1084_copy_o27023,NovaSeq_20211220_NOV1084_copy_o26977,NovaSeq_20211220_NOV1084_copy_o27026,NovaSeq_20211223_NOV1088_o27040_DataDelivery,NovaSeq_20211223_NOV1088_o27023,NovaSeq_20211223_NOV1088_o26977,NovaSeq_20211223_NOV1088_o27026
## linking instead of copying ?
## --reflink for CoW filesystems (ZFS, BTRFS)
## --hardlink for most unix-like filesystems
link=--link
# parallel copy jobs (default: 16)
parallel=8
# SSH connection timeout (default: 300)
contimeout=300
# IO timeout (default: 300)
iotimeout=300
# number of attempts to reconnect (Default: 10)
#retries=10
# mark bad runs
badlist=MiSeq_210122_MS562_o23881_DataDelivery,Fastqc_53742_2021-01-27--15-56-09,MiSeq_210129_MS564_o23775_DataDelivery,NOV657_COV19_o24384,MiSeq_210317_MS586_ww_o24329_o24329_DataDelivery,NovaSeq_20210806_NOV873_o25679_DataDelivery,NovaSeq_20210806_NOV873_o25697_DataDelivery,Fastqc_64627_2021-12-19--17-54-32,Fastqc_64710_2021-12-22--11-02-11,NovaSeq_20211217_NOV1084_o27040_DataDelivery,NovaSeq_20211217_NOV1084_o26977,NovaSeq_20211217_NOV1084_o27023,NovaSeq_20211217_NOV1084_o27026,Fastqc_64771_2021-12-25--11-15-42,Fastqc_64774_2021-12-25--11-17-46,Fastqc_64703_2021-12-22--10-58-32,Fastqc_64706_2021-12-22--11-00-41,Fastqc_64636_2021-12-19--17-58-55,Fastqc_64713_2021-12-22--11-03-19,Fastqc_64777_2021-12-25--11-19-09,Fastqc_64630_2021-12-19--17-56-31,Fastqc_64780_2021-12-25--11-20-17,Fastqc_64633_2021-12-19--17-57-51,NovaSeq_20221007_NOV1461_o29645_DataDelivery
forcelist=NOV641,NOV674_COV19_repeats,NOV741_COVID
# if libkit isn't mentionned, set protocol to this:
fallbackproto=v41
# do we download patchmap lists from google sheet?
google_sheet_patches=0