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merge nextflow_conversion branch to main #83

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merged 150 commits into from
Aug 29, 2024
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d2f061e
ADD INDEX_VCF process
hyunhwan-bcm May 22, 2024
b9ee913
added pre-processing process
hyunhwan-bcm May 22, 2024
4a4bd41
change dirname run -> script.
hyunhwan-bcm May 23, 2024
dc6728b
added ANNOT PHRANK/ENSMBL
hyunhwan-bcm May 23, 2024
fc9a090
enable docker.
hyunhwan-bcm May 23, 2024
02caca1
add phrank scoring.
hyunhwan-bcm May 23, 2024
1aa5585
arrange newlines.
hyunhwan-bcm May 23, 2024
915d844
add OMIM simmiarity calculation.
hyunhwan-bcm May 23, 2024
6cdc51a
add OMIM and HPO refs.
hyunhwan-bcm May 23, 2024
5d5822c
change for file paths.
hyunhwan-bcm May 23, 2024
411232c
add output paths.
hyunhwan-bcm May 23, 2024
43af2f2
forgot to add genemap2 path.
hyunhwan-bcm May 23, 2024
faf3b95
add PHRANK SCORING and HPO SIM calc.
hyunhwan-bcm May 24, 2024
ef5dc97
add GNOMAD references
hyunhwan-bcm May 24, 2024
3c3686d
add FILTER_PROBAND
hyunhwan-bcm May 24, 2024
67cf7c7
add VEP_ANNOTATE
hyunhwan-bcm May 24, 2024
a2d570f
not sure why is is not working.
hyunhwan-bcm May 24, 2024
840c577
it was a problem for parameters.
hyunhwan-bcm May 24, 2024
b638076
let's wait until I get something.
hyunhwan-bcm May 24, 2024
036a3cf
fix a typo
hyunhwan-bcm May 28, 2024
0ef7647
fixed another typo
hyunhwan-bcm May 28, 2024
09032c1
found the bug, but haven't compared the output and the other parts.
hyunhwan-bcm May 29, 2024
66e6c82
change the cache mode to lenient.
hyunhwan-bcm May 29, 2024
db05985
change all wildcard to params.run_id
hyunhwan-bcm May 29, 2024
b267689
added prediction, need to validate.
hyunhwan-bcm May 29, 2024
ecad35a
replace phrank scripts to bin.
hyunhwan-bcm May 29, 2024
741cf4a
all scripts have been moved to bin
hyunhwan-bcm May 29, 2024
372dc48
all scripts have been moved to bin
hyunhwan-bcm May 29, 2024
86fcab6
merge
hyunhwan-bcm May 29, 2024
70c49c4
remove __init__.py - empty
hyunhwan-bcm May 30, 2024
5b44d1c
lint the python files.
hyunhwan-bcm May 30, 2024
365775b
lint the R files.
hyunhwan-bcm May 30, 2024
3005db3
stop tracking .gitignore.
hyunhwan-bcm May 30, 2024
64dada6
update .gitignore.
hyunhwan-bcm May 30, 2024
8b7b975
update .gitignore.
hyunhwan-bcm May 30, 2024
304b82f
edit to preserve the selected variants.
hyunhwan-bcm Jun 7, 2024
cda752f
add TODO
hyunhwan-bcm Jun 7, 2024
6cb5d76
change output names to have run_id.
hyunhwan-bcm Jun 7, 2024
a7d28dc
change nextflow.config
hyunhwan-bcm Jun 7, 2024
0ce5e0b
add run_diff to compare outputs.
hyunhwan-bcm Jun 7, 2024
c0abdd8
fix the order.
hyunhwan-bcm Jun 10, 2024
ef362e6
clean-up
hyunhwan-bcm Jun 10, 2024
f846fb3
add errorStrategy.
hyunhwan-bcm Jun 10, 2024
0461fbf
fix paraemter typos.
hyunhwan-bcm Jun 10, 2024
b416d00
clean-up.
hyunhwan-bcm Jun 10, 2024
8acac3e
change the process setup for the Feature Engineering Part 1.
hyunhwan-bcm Jun 14, 2024
43ad5d4
change cpu configure for some processes
hyunhwan-bcm Jun 14, 2024
fc161b3
Update main.nf
hyunhwan-bcm Jun 14, 2024
bf0f296
Merge branch 'nextflow_conversion' of github.com:hyunhwan-bcm/AI_MARR…
hyunhwan-bcm Jun 18, 2024
a706fb1
Handle MT values as -1 to avoid string comparison (#1)
jylee-bcm Jun 18, 2024
ed361df
Refactor prediction step to eliminate multiprocessing (#2)
jylee-bcm Jun 19, 2024
e77b0bb
Merge branch 'nextflow_conversion' of github.com:hyunhwan-bcm/AI_MARR…
hyunhwan-bcm Jun 19, 2024
9d56554
Optimize duplication checking to index-based comparison (#3)
jylee-bcm Jun 20, 2024
f09d6d0
Merge branch 'nextflow_conversion' of github.com:hyunhwan-bcm/AI_MARR…
hyunhwan-bcm Jun 27, 2024
1ac1a55
Optimize process_sample() Function Using Pandas DataFrame (#5)
jylee-bcm Jun 27, 2024
df6b6b3
Removed Multiprocessing from feature.py (#6)
jylee-bcm Jun 27, 2024
e2ffa1a
Merge branch 'nextflow_conversion' of github.com:hyunhwan-bcm/AI_MARR…
hyunhwan-bcm Jun 27, 2024
867c884
Fix vep split (#7)
hyunhwan-bcm Jun 27, 2024
d21702c
Stop generating unused intermediate file (#10)
jylee-bcm Jul 3, 2024
246503e
Optimize Feature Engineering Part 2 (#9)
jylee-bcm Jul 3, 2024
b0ccfa2
Fix a bug that vep splitter didn't work under nextflow env (#8)
jylee-bcm Jul 3, 2024
f9888e1
Untrack Nextflow Config (#11)
jylee-bcm Jul 9, 2024
2525837
Update VarTierDiseaseDBFalse.R To Improve Speed
hyunhwan-bcm Jul 10, 2024
4b4b7b9
remove a code-line for debug
hyunhwan-bcm Jul 10, 2024
d38c15e
Merge branch 'nextflow_conversion' of github.com:hyunhwan-bcm/AI_MARR…
hyunhwan-bcm Jul 11, 2024
2da37a6
Remove unused rundiff.py (#12)
jylee-bcm Jul 12, 2024
b930322
Change library in VarTierDiseaseDBFalse.R (#13)
hyunhwan-bcm Jul 12, 2024
b7e3c6d
remove commented lines. (#14)
hyunhwan-bcm Jul 12, 2024
716bcd5
Filter VCFs to Exonic Regions Only (#17)
jylee-bcm Jul 15, 2024
357939b
Preprocess for normalizing mod5 network (#16)
jylee-bcm Jul 15, 2024
5f19be6
Revert "Filter VCFs to Exonic Regions Only (#17)" (#18)
jylee-bcm Jul 15, 2024
09af85c
Revert "Revert "Filter VCFs to Exonic Regions Only (#17)" (#18)" (#20)
jylee-bcm Jul 15, 2024
3190492
Reorder exonic filtering step to after mitochondria removal (#21)
jylee-bcm Jul 17, 2024
159d7f9
Update bcftools to 1.20 (#22)
jylee-bcm Jul 18, 2024
95af064
Hj/nxf comp/update bivar (#27)
hyunhwan-bcm Aug 1, 2024
c9990ad
Check completed - nextflow comparison with main using hg38 (#25)
hyunhwan-bcm Aug 1, 2024
bda171a
Merge branch 'hyunhwan-bcm-nextflow_conversion' into nextflow_conversion
hyunhwan-bcm Aug 2, 2024
891e7f4
checkout confict files from main
hyunhwan-bcm Aug 2, 2024
73b4b2f
Merge pull request #18 from hyunhwan-bcm/nextflow_conversion
hyunhwan-bcm Aug 2, 2024
aed358c
update bcf_tools version from v1.9 to v1.20.
ZaahidShaik Aug 7, 2024
85de284
Merge pull request #43 from ZaahidShaik/bcf_version_update
hyunhwan-bcm Aug 7, 2024
a41b8f7
Create module 3 and split into smaller pieces
jylee-bcm Aug 12, 2024
56a2c66
Separate decipher part
jylee-bcm Aug 12, 2024
cd13c3e
Separate gnomad and omim
jylee-bcm Aug 12, 2024
63176fe
Comment out not informative comments
jylee-bcm Aug 12, 2024
064fe95
Remove module list dependencies from the annotate functions
jylee-bcm Aug 12, 2024
de12028
Copy only necessary part.
jylee-bcm Aug 13, 2024
fa4c32c
Merge pull request #46 from LiuzLab/feateng1
hyunhwan-bcm Aug 13, 2024
ac49af6
Add Bed Filter Parameter and Close #48
jylee-bcm Aug 13, 2024
6d8759c
Merge pull request #50 from LiuzLab/bed_filter
hyunhwan-bcm Aug 14, 2024
03bf92a
Add --help flag for displaying usage information to users.
ZaahidShaik Aug 14, 2024
7546d7b
Fixing changes.
ZaahidShaik Aug 14, 2024
07c75e0
Merge pull request #51 from ZaahidShaik/add_help_option
hyunhwan-bcm Aug 14, 2024
ab61010
change split by chromosome.
hyunhwan-bcm Aug 15, 2024
d87ed4a
change split by chromosome.
hyunhwan-bcm Aug 15, 2024
0b3e299
remove redundant run directory.
hyunhwan-bcm Aug 15, 2024
e4274dc
remove the previous split script.
hyunhwan-bcm Aug 15, 2024
73d5b6b
fix some bugs
hyunhwan-bcm Aug 15, 2024
329eb71
fix the issue with `head` -> `tail`
hyunhwan-bcm Aug 15, 2024
04e4f07
change to process for each chromosome.
hyunhwan-bcm Aug 15, 2024
5b8c651
Add GVCF to VCF logic. Close #56
jylee-bcm Aug 15, 2024
658fdbb
Merge pull request #58 from LiuzLab/issue56
hyunhwan-bcm Aug 15, 2024
5349efc
Add validation for required inputs types and error_messages before wo…
ZaahidShaik Aug 16, 2024
73c5aed
Merge pull request #60 from ZaahidShaik/groovy_add_params_validation
hyunhwan-bcm Aug 16, 2024
49dd7ce
Optimize HGMD information search in Feature Engineering Part 1
jylee-bcm Aug 19, 2024
d04d442
Merge pull request #61 from LiuzLab/fe1
hyunhwan-bcm Aug 19, 2024
a876e49
Merge pull request #57 from LiuzLab/hj/chr_separation
hyunhwan-bcm Aug 19, 2024
9a7fbe8
Revert "job separation by chromosome"
hyunhwan-bcm Aug 19, 2024
e7b5954
Merge pull request #62 from LiuzLab/revert-57-hj/chr_separation
hyunhwan-bcm Aug 19, 2024
4331002
Revert "Revert "job separation by chromosome""
hyunhwan-bcm Aug 19, 2024
a6f25a4
Use function naming rule for functions in workflow file
jylee-bcm Aug 19, 2024
18d5f0c
Use named output for every process
jylee-bcm Aug 19, 2024
5d9c2e6
Delete run/data_dependencies
jylee-bcm Aug 19, 2024
0ce4a36
Merge pull request #65 from LiuzLab/cleanmain
hyunhwan-bcm Aug 19, 2024
ef7cef8
remove comments in fillna_tier.py
hyunhwan-bcm Aug 20, 2024
64aad29
separate generate_new_matrix_2.py
hyunhwan-bcm Aug 20, 2024
f9c5dcc
revamp the workflow.
hyunhwan-bcm Aug 20, 2024
a50e11c
change the default parameter for cpu and memory.
hyunhwan-bcm Aug 20, 2024
414f8d4
Merge branch 'nextflow_conversion' into revert-62-revert-57-hj/chr_se…
hyunhwan-bcm Aug 20, 2024
c8a0532
remove cpu 1 from VEP_ANNOTATE
hyunhwan-bcm Aug 20, 2024
083ad92
Merge branch 'revert-62-revert-57-hj/chr_separation' of github.com:Li…
hyunhwan-bcm Aug 20, 2024
ebf3a31
change the variable name in PREDICTION
hyunhwan-bcm Aug 20, 2024
8473ba7
Merge pull request #63 from LiuzLab/revert-62-revert-57-hj/chr_separa…
hyunhwan-bcm Aug 20, 2024
7dc1a63
Rename and Regroup Processes More Meaningfully
jylee-bcm Aug 20, 2024
4322853
fix phrank error.
hyunhwan-bcm Aug 21, 2024
c74616f
Merge pull request #69 from LiuzLab/hj/fix_phrank_error
arine Aug 21, 2024
935f979
Rename based on the feedback 1
jylee-bcm Aug 21, 2024
005e4c6
Merge pull request #68 from LiuzLab/meaningful-names
hyunhwan-bcm Aug 21, 2024
294706d
fix empty HPO error.
hyunhwan-bcm Aug 22, 2024
64750e8
make the same as the processing in
hyunhwan-bcm Aug 22, 2024
b98dbc0
Merge pull request #72 from LiuzLab/hj/fix_empty_hpo
arine Aug 23, 2024
fd930fc
update the manual for nextflow version.
hyunhwan-bcm Aug 26, 2024
2dd3489
apply rst format.
hyunhwan-bcm Aug 26, 2024
21fee78
fix code block format.
hyunhwan-bcm Aug 26, 2024
d662d00
Merge branch 'nextflow_conversion' into hj/rst_update
hyunhwan-bcm Aug 26, 2024
232efad
Merge pull request #73 from LiuzLab/hj/rst_update
ChaozhongLiu Aug 26, 2024
d9d3d39
Revert "Manual update"
hyunhwan-bcm Aug 26, 2024
432edcf
took alternative way to enable --help.
hyunhwan-bcm Aug 26, 2024
0061fa9
add bed_filter to nf_usage.
hyunhwan-bcm Aug 26, 2024
c36ca70
Merge pull request #74 from LiuzLab/revert-73-hj/rst_update
ChaozhongLiu Aug 26, 2024
c3bb8c9
Merge pull request #75 from LiuzLab/hj/fix_config
ZaahidShaik Aug 26, 2024
deba71f
Organize the use of out_dir
jylee-bcm Aug 26, 2024
ce3b88c
Update README and Version Command
jylee-bcm Aug 27, 2024
362311a
doc: fix installation.rst indentation
arine Aug 27, 2024
30a1fd2
doc: fix DOI link
arine Aug 27, 2024
ef2d7fc
doc: fix code block and header at installation.rst
arine Aug 27, 2024
fd08156
Merge pull request #78 from LiuzLab/readme
arine Aug 27, 2024
c2bbaa2
Merge pull request #76 from LiuzLab/outdirrunid
jylee-bcm Aug 28, 2024
ea84623
doc: update S3 URI at installation.rst
arine Aug 28, 2024
686b13b
Merge pull request #82 from LiuzLab/readme-2
jylee-bcm Aug 28, 2024
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doc: fix DOI link
arine authored Aug 27, 2024

Verified

This commit was signed with the committer’s verified signature.
DRSchlaubi Michael Rittmeister
commit 30a1fd245ccff7a0cc703ac58e19a5e9a367d37d
5 changes: 3 additions & 2 deletions docs/source/index.rst
Original file line number Diff line number Diff line change
@@ -30,7 +30,8 @@ Citation

Mao, D., Liu, C., Wang, L., AI-Ouran, R., Deisseroth, C., Pasupuleti, S., Kim, S. Y., Li, L., Rosenfeld, J. A., Meng, L., B
urrage, L. C., Wangler, M. F., Yamamoto, S., Santana, M., Perez, V., Shukla, P., Eng, C. M., Lee, B., Yuan, B., … Liu, Z. (2024).
**AI-MARRVEL—A knowledge-driven ai system for diagnosing mendelian disorders. NEJM AI, 1(5).** <a href="https://doi.org/10.1056/AIoa2300009">https://doi.org/10.1056/AIoa2300009</a>
**AI-MARRVEL—A knowledge-driven ai system for diagnosing mendelian disorders. NEJM AI, 1(5).** DOI: `10.1056/AIoa2300009
<https://doi.org/10.1056/AIoa2300009>`_


License
@@ -45,4 +46,4 @@ AI-MARRVEL is licensed under `GPL-3.0 <https://github.com/LiuzLab/AI_MARRVEL/blo
installation
runningaim
input
output
output