InPreD PRONTO issues - Githubissues

InPreD / PRONTO

rePort geneRator fOr iNpred Tumor bOards

GNU General Public License v3.0

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All the textbox6 related commands could go to a new function called something like `set_layout_textbox_tumor_content`. Similarly, commands related to other textboxes could be split to smaller functions with meaningful naming.

#47 xiaoliz0 opened 3 weeks ago
0
It would be nice to separate 'graphical' and 'functional' parts of the code to separate functions. I know this is quite some work, but I also believe it would be worth from the perspective of readability.

#46 xiaoliz0 opened 3 weeks ago
0
just a practical question, why do not impress sites get an empty string `""` and impress sites `Inclusion site`. Would it be better to maybe clearly state that it is impress or not? But I am not sure how you handle this downstream, maybe it will change a lot.

#45 xiaoliz0 opened 3 weeks ago
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I understand that these are all column names? Maybe they can be collected in an object?

#44 xiaoliz0 opened 3 weeks ago
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Suggestion from Tina

#43 xiaoliz0 opened 1 month ago
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Suggestion from Jone

#42 xiaoliz0 opened 1 month ago
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Typing error for "target_cod_region"

#41 xiaoliz0 opened 1 month ago
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Suggestion from Martin for file opening function

#40 xiaoliz0 opened 1 month ago
1
Extract the inclusion_site information from the code to config file.

#39 xiaoliz0 opened 1 month ago
1
Move "import" module from function to the top of script.

#38 xiaoliz0 opened 1 month ago
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Tumor content number provided multiple times for one sample set

#37 tinavisnovska opened 2 months ago
3
Updates from develop_OUS to main

#36 xiaoliz0 closed 3 weeks ago
4
New function request

#35 xiaoliz0 closed 3 months ago
1
Report data error instead of crashing

#34 xiaoliz0 closed 3 months ago
1
Encoding issue with PRONTO metadata input file

#33 tinavisnovska closed 3 months ago
2
MTF version 2023 & 2024

#32 xiaoliz0 closed 3 months ago
1
suggestion: treat the empty lines in the metadata file the same way as comments

#30 tinavisnovska closed 3 months ago
4
generating a report for DNA and RNA sample from different runs - does not work properly when the DNA seq run is older than the RNA seq run

#29 tinavisnovska closed 4 months ago
5
fix: to read characters æ,å,ø; specify file encoding as 'ISO-8859-1'

#28 gertrudeln closed 5 months ago
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Considering switching over to python image with pip instead of the miniconda image

#27 marrip opened 5 months ago
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Bool reads `Faulse` in the `configure_PRONTO.ini` file

#26 marrip closed 5 months ago
3
chore: add devcontainer

#25 marrip closed 5 months ago
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tagged images not available on dockerhub

#24 marrip closed 5 months ago
3
PRONTO failing without clear error message when encountering an empty small variant table

#23 marrip closed 5 months ago
3
Expansion, re-wording and re-formatting of README.md

#22 tinavisnovska closed 5 months ago
0
no license in the repository

#21 tinavisnovska closed 3 months ago
3
PRONTO can not read characters “æ, ø and å” in the meta file

#20 xiaoliz0 closed 5 months ago
0
Crash when DNA and RNA for a sample are from different runs

#17 torben-uio closed 7 months ago
1
sys.exit(0) when exiting on error

#16 tinavisnovska closed 7 months ago
3
DNA_sampleID_format causing warnings for every other node than OUS

#15 tinavisnovska closed 5 months ago
1
pptx template inconsistency, slides 1, 6 and 7

#14 tinavisnovska closed 7 months ago
1
tumor site vs. diagnosis in the pptx template

#13 tinavisnovska closed 7 months ago
1
missing documentation of "-m" and "-c" options and related file formats

#12 tinavisnovska closed 7 months ago
1
Update README.md

#11 torbenlu closed 7 months ago
1
The first template slide does not make sense if the clinical info is provided via the metadata file

#10 tinavisnovska closed 7 months ago
1
add expected file names into a ChangeLog when they changed

#9 tinavisnovska closed 7 months ago
1
In/InPreD_PRONTO_metadata.txt

#8 tinavisnovska closed 7 months ago
1
genomics core facility, OUS in the default template

#7 tinavisnovska closed 7 months ago
1
Check existence of InPreD_clinical_data_file when generating RNA_ori_name in PRONTO.py

#6 tinavisnovska closed 7 months ago
1
Missing file [sample]_CNV_overview_plots.pdf in test data

#5 gertrudeln closed 7 months ago
1