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Version sync #14

Merged
merged 66 commits into from
Dec 12, 2021
Merged

Version sync #14

merged 66 commits into from
Dec 12, 2021

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chuan-wang
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ssjunnebo and others added 30 commits October 14, 2020 09:51
@ssjunnebo
Merge pull request #293 from chuan-wang/master
bded2b0 
Add support for Smart-seq index sets
@ssjunnebo
Merge pull request #294 from chuan-wang/master
084da7f 
Fix issue that free space on NAS is not correctly parsed after server…
@ssjunnebo
Merge pull request #295 from chuan-wang/master
07f86e8 
Change the way how samples are sorted
@aanil
Merge pull request #296 from chuan-wang/master
eb5265c 
Support NextSeq 2000
@aanil
Merge pull request #297 from chuan-wang/master
e8df5d5 
Fix FC name pattern for NextSeq2000; Setup VERSIONLOG.md
@chuan-wang
Merge pull request #298 from chuan-wang/master
6cc5ea8 
Support addtional 10X index types
@chuan-wang
Merge pull request #299 from chuan-wang/master
ee5fb5c 
Support different FC ID pattern for NextSeq2000
@aanil
Merge pull request #300 from chuan-wang/master
1d38b9e 
Support different FC ID pattern for NextSeq2000 in bioinfo_tab.py
@chuan-wang
Merge pull request #301 from chuan-wang/master
d216226 
Small adjust of 10X ATACseq masks
@chuan-wang
Merge pull request #303 from chuan-wang/master
93ecc09 
Handle special case with index2 only
@chuan-wang
Merge pull request #304 from chuan-wang/master
ffff011 
Support addtional 10X index types
@chuan-wang
Merge pull request #305 from chuan-wang/master
c157d72 
Fix bugs
@chuan-wang
Merge pull request #306 from chuan-wang/master
c336c9f 
Handle special case with index 2 only for NovaSeq
@chuan-wang
Merge pull request #307 from chuan-wang/master
41377c8 
Allow 0 mismatch in demux for short single index
@ssjunnebo
Initial setup for ONT refactor
4ed4a7b
@ssjunnebo
Reorganise nanopore code into classes
a8169aa
@ssjunnebo
Refactor minion processing
7051933
@ssjunnebo
Some fixes from testing
4d4a0fc
@chuan-wang
Merge pull request #308 from chuan-wang/master
0de0e90 
Specify CopyComplete.txt as indicator for cleaning NovaSeq runs
@ssjunnebo
rename flowcell_id
3a56cd9
@ssjunnebo
Skip some non-data dirs
7ed7203
@ssjunnebo
Don't start nanoseq if sequencing is running
53e6db1
@ssjunnebo
Only start one nanoseq run at a time
eeedaba
@ssjunnebo
Use pathlib to get dir to archive
8ebb849
@ssjunnebo
Refactor analysis tests
87c8854
@ssjunnebo
Refactor MinION tests
f41ffcc
@ssjunnebo
Merge branch 'master' of https://github.com/SciLifeLab/TACA into prom…
06df9b1 
…ethion
@ssjunnebo
Versioning
295a98f
@ssjunnebo
remove old file
6ca1238
@ssjunnebo
Process promethion data
1d97c9f
ssjunnebo and others added 28 commits October 26, 2021 15:41
@ssjunnebo
Make calling methods aware of errors
dc1c096
@ssjunnebo
Remove empty returns
b3411a7
@parlundin
Merge pull request #310 from ssjunnebo/python3_fixes
9160d4a 
Fix encoding issue for py3
@ssjunnebo
else instead of returns
1a40187
@ssjunnebo
Have copy_results_for_lims return true or false
59db267
@ssjunnebo
Fix nanopore tests
8a6e290
@alneberg
Merge pull request #309 from ssjunnebo/promethion
1be99be 
Refactor MinION analysis and add PromethION transfer
@ssjunnebo
Set run type based on LIMS sample sheet
c6a3c68
@ssjunnebo
Only work on run with lims sample sheet generated
626f0cb
@ssjunnebo
Get nanopore tests to pass
7957f18
@ssjunnebo
decode byte string
e207005
@aanil
Merge pull request #312 from ssjunnebo/preproc_py3
3314ebb 
decode byte string
@remiolsen
Merge pull request #311 from ssjunnebo/minion_non_qc
f0d62a2 
Automatically detect minion run type
@ssjunnebo
Ignore .nextflow dir and stray files
01178b4
@ssjunnebo
style fixes
521eff9
@alneberg
Merge pull request #313 from ssjunnebo/squiggle_dirs
704929e 
Ignore .nextflow dir and stray files
@ssjunnebo
Only run TACA on MinION QC runs
d6bd37d
@ssjunnebo
Fix tests
f1de0f2
@ssjunnebo
Versioning
a88c144
@ssjunnebo
Update samplesheet for new nanoseq version
0f2775d
@ssjunnebo
Clarify log message
839a1a7
@aanil
Merge pull request #314 from ssjunnebo/minion_qc_refactor
f756547 
Minion qc refactor
@ssjunnebo
Updates for nanoseq 2.0.1
78f9c76
@ssjunnebo
Fix typo
1d8ae00
@ssjunnebo
Add mandatory --protocol option
fd03be6
@ssjunnebo
Fix tests
b98bb61
@ssjunnebo
Bump version
90606df
@chuan-wang
Merge pull request #315 from ssjunnebo/nanoseq_sample_sheet_update
3361db2 
Nanoseq sample sheet update
@chuan-wang chuan-wang merged commit a19083b into chuan-wang:master Dec 12, 2021
chuan-wang pushed a commit that referenced this pull request Oct 8, 2024
@ssjunnebo
Merge pull request #14 from kedhammar/ssjunnebo_aviti
89e4236 
Clarify get_mask() and also use it to generate R1/R2 masks
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6 participants
@chuan-wang @ssjunnebo @aanil @parlundin @alneberg @remiolsen