Add GVCF to VCF logic. Close #56

[jylee-bcm]

Changes

• Build fasta files (.fa, .fai, .dict) at the path of ./out/reference_index when it didn't produce it before
• Utilize gatk commands from the broadinstitute/gatk from dockerhub
• Split VCF_PREPROCESS into two, one is for gatk, the other is for the as it did.

Testing

• Use the vcf file of /home/jaeyeon/Data/aim_test/gvcf.vcf.gz in elpaso server.

[hyunhwan-bcm]

LGTM

[hyunhwan-bcm]

what's this?

[jylee-bcm]

vscode complained with the following error, so that was resolved by this config file

2024-08-15 16:29:35.802 [info] [Error - 4:29:35 PM] (1950325) Enumeration of workspace source files is taking longer than 10 seconds.
This may be because:
* You have opened your home directory or entire hard drive as a workspace
* Your workspace contains a very large number of directories and files
* Your workspace contains a symlink to a directory with many files
* Your workspace is remote, and file enumeration is slow
To reduce this time, open a workspace directory with fewer files or add a pyrightconfig.json configuration file with an "exclude" section to exclude subdirectories from your workspace. For more details, refer to https://github.com/microsoft/pyright/blob/main/docs/configuration.md.

[hyunhwan-bcm]

Got it. Thanks From: Jaeyeon Lee ***@***.***> Date: Thursday, August 15, 2024 at 4:58 PM To: LiuzLab/AI_MARRVEL ***@***.***> Cc: Jeong, Hyun-Hwan ***@***.***>, Review requested ***@***.***> Subject: Re: [LiuzLab/AI_MARRVEL] Add GVCF to VCF logic. Close #56 (PR #58) ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.

…

________________________________ @jylee-bcm commented on this pull request.

________________________________ On pyrightconfig.json<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LiuzLab_AI-5FMARRVEL_pull_58-23discussion-5Fr1719052356&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=-lih8OIo66XtgJH6zqJrfjIwRtqkkhDYbiD5mmg9N6M&m=VUNJAbs4vAMy_XRGYykvH04zvG8mXTlRzcn-QplAgsiYSqxgWnFNT3ot3LrY-xig&s=d9_JvJnyNAwerGXmg1_6Ot_EY4ZIi0JNztyu3SWeH2k&e=>: vscode complained with the following error, so that was resolved by this config file 2024-08-15 16:29:35.802 [info] [Error - 4:29:35 PM] (1950325) Enumeration of workspace source files is taking longer than 10 seconds. This may be because: * You have opened your home directory or entire hard drive as a workspace * Your workspace contains a very large number of directories and files * Your workspace contains a symlink to a directory with many files * Your workspace is remote, and file enumeration is slow To reduce this time, open a workspace directory with fewer files or add a pyrightconfig.json configuration file with an "exclude" section to exclude subdirectories from your workspace. For more details, refer to https://github.com/microsoft/pyright/blob/main/docs/configuration.md. — Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LiuzLab_AI-5FMARRVEL_pull_58-23discussion-5Fr1719052356&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=-lih8OIo66XtgJH6zqJrfjIwRtqkkhDYbiD5mmg9N6M&m=VUNJAbs4vAMy_XRGYykvH04zvG8mXTlRzcn-QplAgsiYSqxgWnFNT3ot3LrY-xig&s=d9_JvJnyNAwerGXmg1_6Ot_EY4ZIi0JNztyu3SWeH2k&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_BHZAYJBN7J2Z7YNVZQNVCQDZRUP6LAVCNFSM6AAAAABMS6WMH6VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDENBRGQZDANZTGM&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=-lih8OIo66XtgJH6zqJrfjIwRtqkkhDYbiD5mmg9N6M&m=VUNJAbs4vAMy_XRGYykvH04zvG8mXTlRzcn-QplAgsiYSqxgWnFNT3ot3LrY-xig&s=NJE8oX-QhoNW4xKnVPcVtD7gdc3mU9_n8BUeie-BTvM&e=>. You are receiving this because your review was requested.Message ID: ***@***.***>