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LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis
GNU General Public License v3.0
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Nextflow conversion #18

Closed hyunhwan-bcm closed 3 months ago

hyunhwan-bcm commented 5 months ago

The PR includes numerous changes and should be carefully reviewed. @sasidharPasupuleti and @ZaahidShaik, please try to run this PR and verify its functionality. It would be beneficial to test it against a previously completed run.

The PR Summary

How to use (or test)

Here is an example:

nextflow run main.nf --run_id 12345 --ref_ver "hg19" --outdir testout_061024 \
                                    --input_hpo /home/hwan/AI_MARRVEL/test_data/hpos.txt \
                                    --input_vcf /home/hwan/AI_MARRVEL/test_data/demo.vcf.gz \
                                    --ref_dir /home/hwan/aim_data_dependencies_04_24_2024_sasi

You can also change the parameters in nextflow.config - you can run nextflow run main.nf

hyunhwan-bcm commented 4 months ago

@jylee-bcm please review my latest commit to this branch.

hyunhwan-bcm commented 4 months ago

I thought I remove them, but it wasn't pushed. I am fine that if you delete the directory.

jylee-bcm commented 4 months ago

I thought I remove them, but it wasn't pushed. I am fine that if you delete the directory. You were right, just git couldn't track the difference.

hyunhwan-bcm commented 4 months ago

You can remove it just for comparison of every column of dataframes

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From: Jaeyeon Lee @.> Sent: Friday, July 12, 2024 11:46:43 AM To: LiuzLab/AI_MARRVEL @.> Cc: Jeong, Hyun-Hwan @.>; Author @.> Subject: Re: [LiuzLab/AI_MARRVEL] Nextflow conversion (PR #18)

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@jylee-bcm commented on this pull request.

On utils/run_diff.pyhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LiuzLab_AI-5FMARRVEL_pull_18-23discussion-5Fr1676191866&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=-lih8OIo66XtgJH6zqJrfjIwRtqkkhDYbiD5mmg9N6M&m=2XM5e49yxOQhs1NNB4SFoGxj8unTaRLRVGntuz7wnTDY0WvZgWrEuhHM-xf7btMe&s=CdcZ_jtWIDD_2TTxmQ-_uEx2wfQOROk4kegA_jx-4T4&e=:

Is it actively used? if not, remove it

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