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NorwegianVeterinaryInstitute
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DemultiplexRawSequenceData
A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards
GNU General Public License v3.0
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feature request: If 240126_M06578_0189_000000000-LCLVV_demultiplex\Reports\html\index.html reports zero reads, warn users of error with sample
#81
georgemarselis-nvi
opened
2 months ago
0
test: check that the outputted hash files pass the md5sum -c / sha512sum -c sniff test
#80
georgemarselis-nvi
opened
8 months ago
0
feature request: detect when a run needs to be demultiplexed as single lane
#79
georgemarselis-nvi
opened
8 months ago
0
test: check that the calculated hashlib.md5 and hashlib.sha512 are 128 and 64 bytes respectively
#78
georgemarselis-nvi
opened
9 months ago
1
test: do the calculated hashlib.md5( filetobehashed ).hexdigest( ) / hashlib.sha256( filetobehashed ).hexdigest( ) match what md5sum -c <fileToBeChecked.md5> / sha512sum -c <fileToBeChecked.sha512> outputs?
#77
georgemarselis-nvi
closed
8 months ago
1
sha512sum = hashlib.sha256( filetobehashed ).hexdigest( )
#76
georgemarselis-nvi
closed
9 months ago
4
new feature: mechanism to perform file and directory permission normalization within /rawdata
#75
georgemarselis-nvi
opened
9 months ago
0
new feature: FIle names missing a "." after the Sequencer ID
#74
ajkarloss
opened
9 months ago
1
os.chmod( demux.sampleSheetFilePath, currentPermissions & ~stat.S_IEXEC ) # demux.SampleSheetFilePath is probably +x, remnant from windows transfer, so remove execute bit ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 1] Operation not permitted: '/data/rawdata/230919_M06578_0168_000000000-DHTMT/SampleSheet.csv'
#73
georgemarselis-nvi
closed
9 months ago
1
Instructions for NIRD transfer
#72
magnulei
closed
9 months ago
4
bug: .md5 files and .sha512 files are not written correctly
#71
georgemarselis-nvi
opened
10 months ago
4
Changing name on files after demultiplexing and transfer to NIRD/VIGAS
#70
CathrineAB
closed
10 months ago
2
extra, empty nameProjectList[] item, always last, always empty. should not be there.
#69
georgemarselis-nvi
closed
10 months ago
1
feature request: Get demultiplexing script to calculate coverage for each sample
#68
karinlag
opened
1 year ago
18
bug: Some software save values quoted and prevent the code of getting the index of demux.Sample_Sheet
#67
georgemarselis-nvi
closed
1 year ago
3
discussion: 221124_M06578_0124_000000000-KNW3P Sample_Project name: 12160-123-ringtest ?
#66
georgemarselis-nvi
closed
1 year ago
5
.add() -> .append() that always gets me
#65
georgemarselis-nvi
closed
1 year ago
0
25 check if tar files can be unpacked correctly and with no errors
#64
georgemarselis-nvi
closed
1 year ago
0
discussion: what does demultiplexing do, if a project duplicate is found?
#63
georgemarselis-nvi
closed
1 year ago
3
feature request: implement unit testing
#62
georgemarselis-nvi
opened
1 year ago
0
feature request: break script into python modules
#61
georgemarselis-nvi
opened
1 year ago
0
feature request: add --remove <RunID>/ --remove-demux <RunID> / --rename <RunID>/<Sample> / --remove-fortransfer <RunID> / --(re)upload-nird <RunID> / --(re)upload-vigasp <RunID>
#60
georgemarselis-nvi
opened
1 year ago
2
feature request: time() everything
#59
georgemarselis-nvi
opened
1 year ago
1
16 feature request logging
#58
georgemarselis-nvi
closed
1 year ago
0
testing: How should we handle testing for v1.0
#57
georgemarselis-nvi
opened
1 year ago
14
feature request: notify which samples do not give their _2 side
#56
georgemarselis-nvi
opened
1 year ago
0
feature request: adjust fastqc -t switch according to the CPUs available in the system
#55
georgemarselis-nvi
opened
1 year ago
3
bug: before creating any file structure, ensure the project name exists in /data/rawdata
#54
georgemarselis-nvi
opened
1 year ago
0
feature request: Ansible script that installs FastQC and changes the "processes" variable in the startup script from 4 to nCPUs
#53
georgemarselis-nvi
opened
1 year ago
1
feature request: Ansible script to install MultiQC from pip3
#52
georgemarselis-nvi
opened
1 year ago
0
feature request: investigate if multiqc can use multiple CPUs
#51
georgemarselis-nvi
opened
1 year ago
0
bug: ignore Control Projects
#50
georgemarselis-nvi
opened
1 year ago
1
feature requests Control Projects QC
#49
georgemarselis-nvi
opened
1 year ago
0
feature request: verify crypto signature of any retrieved tar file
#48
georgemarselis-nvi
opened
1 year ago
0
feature request: cryptosign the outgoing tar files using openssl.
#47
georgemarselis-nvi
opened
1 year ago
0
bug: fix output formatting
#46
georgemarselis-nvi
closed
1 year ago
1
QC for control projects
#45
georgemarselis-nvi
closed
1 year ago
1
feature request: email QC report for either the specific project or the control project
#44
georgemarselis-nvi
opened
1 year ago
0
bug: if a project has no *fastq.gz files, do not upload it.
#43
georgemarselis-nvi
opened
1 year ago
1
if a project directory does not contain any CompressedFastQFiles, notify via email, but go on executing.
#42
georgemarselis-nvi
opened
1 year ago
0
not relevant here but equally important: have nagios? notifcation of Cathrine that it is ok for nextseq/miseq to write to seqtech01
#41
georgemarselis-nvi
opened
1 year ago
0
feature request: Have Workplace/Teams chatbot report status of demultiplexing/sequencing
#40
georgemarselis-nvi
opened
1 year ago
0
feature request: SampleSheet.csv should contain the genus name
#39
georgemarselis-nvi
opened
1 year ago
0
feature request: Nanopore data handling AT SOME POINT IN THE FAR FUTURE
#38
georgemarselis-nvi
opened
1 year ago
1
feature request: Detect failed runs for MiSeq/NexSeq
#37
georgemarselis-nvi
opened
1 year ago
3
for_transfer/RunID : put tar files in the same directory
#36
georgemarselis-nvi
closed
1 year ago
1
feature request: Notifications on Workplace
#35
georgemarselis-nvi
opened
1 year ago
1
feature Request: WARN() about diff RawDataDir and DemultiplexDir
#34
georgemarselis-nvi
opened
1 year ago
0
def calcFileHash( DemultiplexRunID ) : do not hash any existing .md5 or .sha512 files present, but do report them
#33
georgemarselis-nvi
closed
8 months ago
2
DemultiplexComplete.txt does not have the right file permissions after demux script finishes
#32
georgemarselis-nvi
closed
1 year ago
3
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