Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ONT update #321

Merged
merged 249 commits into from
May 2, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
249 commits
Select commit Hold shift + click to select a range
0ed13ca
wip
kedhammar Feb 14, 2024
1f704a2
clean up docs
kedhammar Feb 14, 2024
c553497
wip
kedhammar Feb 15, 2024
3cebf81
wip
kedhammar Feb 15, 2024
e01abb8
improve docs and annotation
kedhammar Feb 15, 2024
911bc89
docs
kedhammar Feb 15, 2024
1f86578
docs
kedhammar Feb 15, 2024
dc28478
wip
kedhammar Feb 15, 2024
8b19070
fix typo
kedhammar Feb 15, 2024
c71536a
wip
kedhammar Feb 15, 2024
257b1ce
docs
kedhammar Feb 15, 2024
4dc458d
dump to stderr
kedhammar Feb 15, 2024
5fe1bef
try different sys exit
kedhammar Feb 15, 2024
abfa8b9
test sys exit
kedhammar Feb 15, 2024
e041b7c
harmonize
kedhammar Feb 15, 2024
e8b9e60
follow up on failures
kedhammar Feb 15, 2024
684f32c
improve docs
kedhammar Feb 15, 2024
f6c2698
docs
kedhammar Feb 16, 2024
42edd25
wip
kedhammar Feb 16, 2024
f560a1c
improve step assertion
kedhammar Feb 16, 2024
9def8e9
annotation
kedhammar Feb 16, 2024
cfab8d1
bugfix
kedhammar Feb 16, 2024
151a40d
collect more info
kedhammar Feb 16, 2024
37efa5d
wip new script for flexible UDF calcs
kedhammar Feb 16, 2024
7494480
improve docs, assertions, error handling and readability
kedhammar Feb 19, 2024
914839b
fix mistake in args assertion
kedhammar Feb 19, 2024
bf9da3e
bake argument assertions into parser call
kedhammar Feb 19, 2024
91abc97
more complex arg parsing, still need to update calc_input_volumes
kedhammar Feb 20, 2024
581a5e8
make all udfs CLI-based, improve docs
kedhammar Feb 20, 2024
7aa3594
wip
kedhammar Feb 20, 2024
da2fcf1
remove trace
kedhammar Feb 20, 2024
ec6ac55
:)
kedhammar Feb 20, 2024
c60a89e
need to fix case w/o conc units
kedhammar Feb 20, 2024
a841437
add default conc units udf none
kedhammar Feb 20, 2024
8e69d82
try to accomodate, need testing
kedhammar Feb 20, 2024
abbe634
dump more error info
kedhammar Feb 20, 2024
50b930e
round
kedhammar Feb 20, 2024
a9b2d07
improve, generalize and add new script for amount calc
kedhammar Feb 21, 2024
2292222
generalize script
kedhammar Feb 21, 2024
8f003c9
kill debugger
kedhammar Feb 21, 2024
46d328a
fix docs
kedhammar Feb 21, 2024
4974eb3
bugfix
kedhammar Feb 21, 2024
0367469
add docs
kedhammar Feb 21, 2024
ab1762d
improve logs
kedhammar Feb 21, 2024
1c0515d
improve logging
kedhammar Feb 21, 2024
80ecf1a
more logging
kedhammar Feb 21, 2024
874e66a
fixes
kedhammar Feb 21, 2024
1b946dd
MORE LOGGING
kedhammar Feb 21, 2024
7e22ff2
functioning :) but calculations need double checking and possibly log…
kedhammar Feb 21, 2024
f82cf10
use iteration for udf args definition, untested
kedhammar Feb 21, 2024
3f727cd
document calcs
kedhammar Feb 22, 2024
93eb842
fix calcs
kedhammar Feb 22, 2024
50c460d
start tackling samplesheet generation, separate minknow and anglerfis…
kedhammar Feb 22, 2024
5121af4
add possibility of using step-level UDFs for calculations
kedhammar Feb 22, 2024
8bfed59
wip
kedhammar Feb 22, 2024
d5df1b7
bugfix
kedhammar Feb 23, 2024
e1fed70
namespace fix
kedhammar Feb 23, 2024
40186fa
accomodate fetching and assigning step udfs
kedhammar Feb 26, 2024
ca31ae9
improve docs
kedhammar Feb 26, 2024
376104b
bug squashing
kedhammar Feb 26, 2024
0b385c4
polish logs
kedhammar Feb 26, 2024
eef3370
update docstring
kedhammar Feb 26, 2024
0d15c04
qc arg default false
kedhammar Feb 26, 2024
3279915
docs bump
kedhammar Feb 26, 2024
2ec678a
wip
kedhammar Feb 27, 2024
5cf9eda
wip
kedhammar Feb 27, 2024
6e25efc
wip
kedhammar Feb 27, 2024
35de31a
kill ipdb
kedhammar Feb 27, 2024
ecb0204
improve error handling
kedhammar Feb 27, 2024
4405fa9
reorganize code blocks
kedhammar Feb 27, 2024
1254893
attempt buficks
kedhammar Feb 27, 2024
e467401
bugficks
kedhammar Feb 27, 2024
bb7cbe5
add more log messages
kedhammar Feb 27, 2024
8c71bdf
quotes
kedhammar Feb 27, 2024
0ce5c20
bump docstring and add assertion
kedhammar Feb 27, 2024
adaf81b
improve error handling
kedhammar Feb 27, 2024
892ed04
limit function scope for reusability and improve boilerplate
kedhammar Feb 27, 2024
49cdd9d
restructure anglerfish script (wip)
kedhammar Feb 27, 2024
08f87c2
remove unneccessary assertion
kedhammar Feb 27, 2024
1b9b67e
chaotic progress
kedhammar Feb 27, 2024
033001f
bugfix
kedhammar Feb 27, 2024
5dabf9b
sanitize sample names
kedhammar Feb 27, 2024
84d04e7
catch shutil failing
kedhammar Feb 27, 2024
fccbf04
revert
kedhammar Feb 27, 2024
65dd983
update docs, clean up code
kedhammar Feb 28, 2024
7ea28f3
bugfix
kedhammar Mar 6, 2024
29f43b6
wip equimolar pooling method
kedhammar Mar 6, 2024
c6aacb0
improve error handling and logging
kedhammar Mar 7, 2024
04bed49
refactoring
kedhammar Mar 7, 2024
75820c3
risky refactoring
kedhammar Mar 7, 2024
195117f
improve documentation
kedhammar Mar 7, 2024
e136e1f
fix function application
kedhammar Mar 8, 2024
c740b32
rename module
kedhammar Mar 8, 2024
c8507f8
fix
kedhammar Mar 8, 2024
54a4a91
Add warnings and put UDFs
kedhammar Mar 8, 2024
934332f
mypy, renaming
kedhammar Mar 8, 2024
9bd5eb3
fix module reference
kedhammar Mar 8, 2024
c20f362
add calc method as choice in script args
kedhammar Mar 8, 2024
77c2e62
tyyping fixes
kedhammar Mar 8, 2024
507f04a
fix logic bug
kedhammar Mar 8, 2024
c8cad24
put UDFs
kedhammar Mar 8, 2024
3616afd
bugfix for unspec amount
kedhammar Mar 8, 2024
6d97ea3
add size calculation and improve warning flagging
kedhammar Mar 8, 2024
5ded00b
try highlighting instructions
kedhammar Mar 8, 2024
8db0e2c
minor improvements
kedhammar Mar 11, 2024
81e28cd
more args and logging
kedhammar Mar 11, 2024
e91c128
improve logging
kedhammar Mar 11, 2024
c98cb4e
fix name ref
kedhammar Mar 11, 2024
be08f77
improve error logging
kedhammar Mar 11, 2024
4bf9138
try supressing logs for samplesheet generation when used in assertion
kedhammar Mar 11, 2024
0e18dd2
add logs
kedhammar Mar 11, 2024
3b1ce6a
adapt to new qc wf
kedhammar Mar 11, 2024
0f54d63
expand logging
kedhammar Mar 11, 2024
9280a6e
further adapt
kedhammar Mar 11, 2024
d94dcc0
harmonize qc vs non qc udf handling
kedhammar Mar 11, 2024
2d6b699
fix function argument
kedhammar Mar 11, 2024
484cf67
remove unused imports
kedhammar Mar 12, 2024
3db9c68
try different log format
kedhammar Mar 12, 2024
752a602
reduce logging
kedhammar Mar 12, 2024
46eedab
propagate qc logic
kedhammar Mar 12, 2024
23c2d78
enrich dict
kedhammar Mar 12, 2024
933f2da
rename
kedhammar Mar 12, 2024
68e642f
tryout function for tracking down prior labels to pool of pools
kedhammar Mar 12, 2024
d76206b
simplify functions
kedhammar Mar 13, 2024
5c11b4b
Also return matching inputs when backtracking to specified step
kedhammar Mar 13, 2024
12e5bec
migrate upload_file func outside script
kedhammar Mar 13, 2024
c55c1e9
this one too
kedhammar Mar 13, 2024
4aceed5
Perform adaptive demultiplexing and compille sample-level dataframe
kedhammar Mar 13, 2024
909823d
rename
kedhammar Mar 13, 2024
b68b857
add exc info to error log
kedhammar Mar 13, 2024
8c45910
blind bugfix
kedhammar Mar 13, 2024
4614f09
bugfix
kedhammar Mar 13, 2024
feb0174
add quotes
kedhammar Mar 13, 2024
f1d5ef1
try more advanced logging format
kedhammar Mar 13, 2024
ce17f96
fix logic error
kedhammar Mar 13, 2024
a0edca1
proofing
kedhammar Mar 13, 2024
699d3a7
blind debugging
kedhammar Mar 13, 2024
a429a8b
log file removed via upload func
kedhammar Mar 14, 2024
81ed006
adopt conservative approach to changing function arguments
kedhammar Mar 14, 2024
579c22b
try bugfix
kedhammar Mar 14, 2024
dc7ba90
expand catch
kedhammar Mar 14, 2024
0fcc421
prevent attempted unpacking of None
kedhammar Mar 14, 2024
7d9a6fe
Make sampel-level dataframe compilation independent of qc argument :)
kedhammar Mar 14, 2024
12c1633
bugfix
kedhammar Mar 14, 2024
0e5615b
bugfix
kedhammar Mar 14, 2024
765c459
reformulate assertions to accomodate non-ONT labels
kedhammar Mar 14, 2024
77f05ac
fix flow cell position for non prom fcs
kedhammar Mar 14, 2024
80ca7df
allow traceback func encountering multiple inputs to return successfully
kedhammar Mar 14, 2024
f8766f7
fix handling of non-barcoded illumina libraries
kedhammar Mar 14, 2024
bad3c52
put a pretty df in the logs
kedhammar Mar 14, 2024
3bc556d
add headers
kedhammar Mar 14, 2024
721dddd
ruff 0.3.2
kedhammar Mar 15, 2024
13efcaf
clarify naming
kedhammar Mar 15, 2024
0b68e4c
improve docs and naming
kedhammar Mar 15, 2024
205e9b7
Lot's of changes. Purpose is to automatically detect whether we are g…
kedhammar Mar 15, 2024
ef94766
improve func
kedhammar Mar 15, 2024
3e0434d
remove unused func
kedhammar Mar 15, 2024
1daef73
remove unused import
kedhammar Mar 15, 2024
f6d2762
prevent circular import
kedhammar Mar 15, 2024
aa3d223
fix erroneous reference
kedhammar Mar 15, 2024
da64f88
fix args and typo
kedhammar Mar 18, 2024
00efe1e
try more informative logging
kedhammar Mar 18, 2024
2c6436a
improve logs
kedhammar Mar 18, 2024
2bb62b4
try logging nested breakdown of library contents
kedhammar Mar 27, 2024
2225b81
uniform usage of quotes in log
kedhammar Mar 27, 2024
2f628b3
unclog log
kedhammar Mar 27, 2024
d4e05dd
indent table in log
kedhammar Mar 27, 2024
f7447d2
Make logging the library contents optional
kedhammar Mar 27, 2024
b5ebc2f
bugfix
kedhammar Mar 28, 2024
db6e007
bugfix
kedhammar Mar 28, 2024
a1126e0
assertion
kedhammar Mar 28, 2024
2a68d44
reduce superfluous logging
kedhammar Mar 28, 2024
7bd70f0
clean up operations
kedhammar Mar 28, 2024
bd773d0
add method to summarize a pool with fixed inputs (instead of calculat…
kedhammar Apr 2, 2024
6465c3a
add method as option in cli
kedhammar Apr 2, 2024
f7608c7
typo
kedhammar Apr 2, 2024
f227a77
add file slot
kedhammar Apr 2, 2024
f3b4271
make step traceback accommodate different versions
kedhammar Apr 2, 2024
6edf79c
make ont barcode pattern global variable with capturing groups and si…
kedhammar Apr 2, 2024
d504e21
create in-repo reference for ont barcodes
kedhammar Apr 2, 2024
c8b6e5c
add helpful dicts for navigating barcodes
kedhammar Apr 2, 2024
f20c1cc
typos
kedhammar Apr 2, 2024
19d476a
bugfix
kedhammar Apr 2, 2024
be2ee50
improve readability and docs
kedhammar Apr 2, 2024
f97deea
dirty, dirty wip
kedhammar Apr 2, 2024
d45832e
a new hope
kedhammar Apr 2, 2024
6ffbddc
remove unused arg
kedhammar Apr 2, 2024
2d05af5
simplify logic
kedhammar Apr 2, 2024
5cf3477
derive minknow samplesheet from dataframe
kedhammar Apr 3, 2024
6ad1abc
improve docs, logs and readability
kedhammar Apr 3, 2024
ee4c97d
make args required
kedhammar Apr 3, 2024
6c73993
make db run docs matching agnostic of "QC_" prefix
kedhammar Apr 3, 2024
30ad625
typing
kedhammar Apr 3, 2024
f692688
require args, improve docs
kedhammar Apr 3, 2024
a4a18c0
add todo
kedhammar Apr 3, 2024
ed6d08a
dirty filthy wip
kedhammar Apr 3, 2024
9c4ffa0
simplify samplesheet generation
kedhammar Apr 15, 2024
4fbe531
more logging
kedhammar Apr 15, 2024
93b06b3
major update of parsing script
kedhammar Apr 16, 2024
f4274b8
remove unused
kedhammar Apr 16, 2024
e5506f2
put ONT run name in master step field of analysis step
kedhammar Apr 17, 2024
b776301
add link
kedhammar Apr 17, 2024
4c15138
refactoring, improve logging
kedhammar Apr 17, 2024
7a3fb68
handle no ont bcs
kedhammar Apr 17, 2024
f068ff7
assert sequencing start for qc runs only has one input
kedhammar Apr 17, 2024
2851ab9
bugfix
kedhammar Apr 18, 2024
6d89adb
more logging
kedhammar Apr 18, 2024
9a671e0
fix missing quote
kedhammar Apr 18, 2024
30c9c04
for ont-barcoded pools use sample name as alias, not pool name
kedhammar Apr 18, 2024
190df95
clarify function
kedhammar Apr 19, 2024
d98eecd
don't provide pooling step as argument
kedhammar Apr 19, 2024
0bebe59
remove files after uploading by default
kedhammar Apr 19, 2024
7b9acc2
fix reference
kedhammar Apr 19, 2024
47f4c92
remove superfluous pos arg
kedhammar Apr 19, 2024
e5f9463
revert log removal default
kedhammar Apr 19, 2024
36d9530
simplify differentiating qc runs
kedhammar Apr 19, 2024
d24a47c
propagate arg removal
kedhammar Apr 19, 2024
339da32
more logs
kedhammar Apr 19, 2024
415f626
more logging and remove unused import
kedhammar Apr 19, 2024
f86453b
implicitly evaluate parent process
kedhammar Apr 19, 2024
a08c2cb
clarify log
kedhammar Apr 19, 2024
f9314d4
make step traceback func regex dependent
kedhammar Apr 22, 2024
cf4d7c7
improve logging
kedhammar Apr 22, 2024
09bdf83
write pattern, not object containing pattern
kedhammar Apr 22, 2024
6e460cc
clarify error case
kedhammar Apr 22, 2024
dd5dcfb
add sequencing library name and id to db update
kedhammar Apr 22, 2024
bd1c929
add quotes
kedhammar Apr 22, 2024
aeec114
ruff
kedhammar Apr 22, 2024
7fad247
sort imports
kedhammar Apr 22, 2024
9f868a9
fix mypy issues
kedhammar Apr 22, 2024
68ef2d7
Merge remote-tracking branch 'upstream/master' into ont-new
kedhammar Apr 22, 2024
cacfe29
bump vlog
kedhammar Apr 22, 2024
8eabf23
Merge branch 'master' into ont-new
kedhammar Apr 22, 2024
ef5483a
add docstrings
kedhammar Apr 24, 2024
c703600
improve docstring
kedhammar Apr 24, 2024
7aa41d6
add example
kedhammar Apr 24, 2024
113484b
Provide reassurance of scary function
kedhammar Apr 24, 2024
d912aa8
bump docstring
kedhammar Apr 24, 2024
e510a92
Merge branch 'ont-new' of github.com:kedhammar/scilifelab_epps into o…
kedhammar Apr 24, 2024
77dfb5c
Merge branch 'master' into ont-new
kedhammar Apr 24, 2024
cc787ed
Update scripts/calc_from_args.py
kedhammar Apr 29, 2024
3c1f13e
rename database object variable
kedhammar Apr 29, 2024
df0e8de
Merge branch 'ont-new' of github.com:kedhammar/scilifelab_epps into o…
kedhammar Apr 29, 2024
36ee3ef
add traceback to error logging
kedhammar Apr 29, 2024
646fb92
Merge branch 'master' into ont-new
kedhammar Apr 29, 2024
375a880
prettier
kedhammar Apr 29, 2024
40f8a36
ruff 0.4.2 check
kedhammar Apr 29, 2024
6f6f20d
avoid bare except
kedhammar Apr 29, 2024
1974fe8
Merge branch 'master' into ont-new
kedhammar May 2, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions VERSIONLOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# Scilifelab_epps Version Log

## 20240502.1

Major ONT update and new module 'calc_from_args' for generalized calculations.

## 20240429.1

Add TAKARA_8nt_UDI and TruSeqUDv2-UDI for index checking
Expand Down
1 change: 1 addition & 0 deletions calc_from_args_utils/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
"""Module containing the calculation methods for UDF-agnostic script."""
Loading
Loading