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Clinical-Genomics
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demultiplexing
To keep scripts associated with execution of the Illumina demultiplexing pipeline
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Update CODEOWNERS
#173
pbiology
closed
1 year ago
0
# remove cgstats from demux flows
#172
ChrOertlin
closed
1 year ago
0
Fix(pass environment variable)
#171
karlnyr
closed
1 year ago
0
remove pipefail
#170
karlnyr
closed
1 year ago
1
Fix config files for demultiplexing
#169
beatrizsavinhas
closed
1 year ago
2
passing enviroment variable
#168
gustavlagneborg
closed
1 year ago
1
Bump certifi from 2020.12.5 to 2022.12.7
#167
dependabot[bot]
closed
1 year ago
1
added conda bin environment to scripts, removed scipts/legacy
#166
karlnyr
closed
1 year ago
2
Bump pyyaml from 5.3.1 to 5.4
#165
dependabot[bot]
closed
1 year ago
1
Bump urllib3 from 1.26.2 to 1.26.5
#164
dependabot[bot]
closed
1 year ago
1
Add option to 2500 demux
#163
karlnyr
closed
2 years ago
2
fix(poetry.toml version)
#162
karlnyr
closed
3 years ago
1
Hiseqx never link pooled undetermined
#161
karlnyr
closed
3 years ago
2
Revert "Removing linking of pooled HiSeqX Undermined fastq-files"
#160
karlnyr
closed
3 years ago
0
fix(removed --end option)
#159
karlnyr
closed
3 years ago
2
Removing linking of pooled HiSeqX Undermined fastq-files
#158
karlnyr
closed
3 years ago
0
Standardise the fastq file naming convention
#157
moahaegglund
closed
1 year ago
12
Do not link undetermined HiseqX fastq-files if they are pooled
#156
henrikstranneheim
closed
3 years ago
0
Name the fastq files from HiseqX demux to contain the sample_id as in Novaseq demultiplexing
#155
henrikstranneheim
closed
1 year ago
1
Add Y to base mask
#154
moahaegglund
closed
3 years ago
6
feat(linking of undetermined files)
#153
karlnyr
closed
3 years ago
20
Count read cycles from runParameters.xml
#152
karlnyr
closed
3 years ago
3
fix 2500 sample sheet issues
#151
barrystokman
closed
3 years ago
4
Version check for updates to Novaseq versions
#150
karlnyr
closed
3 years ago
4
Incorrect status of flowcell and now fastq files are linked twice in HK and read count in cgstats is wrong
#149
moahaegglund
closed
1 year ago
11
Fix carriage return in sed command in syncnipt script
#148
barrystokman
closed
3 years ago
3
chmod checkfornewrun.bash
#147
barrystokman
closed
3 years ago
1
fix fluffy basemask issue
#146
barrystokman
closed
3 years ago
3
added option where second index i missing
#145
karlnyr
closed
3 years ago
9
2500 Demultiplexing migration to Hasta
#144
barrystokman
closed
3 years ago
6
Fix/lane count novaseq
#142
karlnyr
closed
3 years ago
4
Create DEPLOYMENT.md
#141
henrikstranneheim
closed
3 years ago
4
fix(novaseq-bind): Add demultiplexed-runs folder to singularity bind…
#140
henrikstranneheim
closed
3 years ago
1
fix weirdness caused by bumpversion typo
#139
barrystokman
closed
3 years ago
3
fix(novaseq_bind_path): Reduce the bind path to simply it and remove …
#138
henrikstranneheim
closed
3 years ago
2
fix novaseq demux script to enable automated post demux actions
#137
barrystokman
closed
3 years ago
3
2500 demultiplexing migration to Hasta
#136
barrystokman
closed
3 years ago
13
Novaseq demultiplexing on Dragen
#135
barrystokman
closed
3 years ago
2
Feat/demux on hasta
#134
barrystokman
closed
3 years ago
4
feat(docker): Adds a bcl2fastq docker recipe
#133
henrikstranneheim
closed
3 years ago
1
WIP Adjust demultiplexing bash scripts so they can run on hasta
#132
barrystokman
closed
3 years ago
2
Hasta demultiplexing test data
#131
barrystokman
closed
3 years ago
1
Change PDC retrieval of 2500/novaseq flowcells destination to hasta instead of thalamus
#130
barrystokman
closed
3 years ago
3
emergency fix index1
#129
barrystokman
closed
3 years ago
1
bug(demux sheet fetch on hasta)
#128
karlnyr
closed
3 years ago
2
Keep Sequencing files for LIMS longer on Thalamus
#127
emmser
closed
3 years ago
2
Feat/indexreport
#126
karlnyr
closed
3 years ago
14
Test bcl2fastq on Hasta
#125
barrystokman
closed
3 years ago
1
Sync flowcells from the NASes to hasta instead of thalamus
#124
barrystokman
closed
2 years ago
0
Add reverse complementing index 2 in samplesheet based on Novaseq Control Software version and reagent kit version
#123
barrystokman
closed
3 years ago
11
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