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.

Sign up for GitHub

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

Jump to bottom

add in processing scripts for human data #40

Merged
merged 33 commits into from
Jul 4, 2024
Merged

add in processing scripts for human data #40

merged 33 commits into from
Jul 4, 2024

Commits on Aug 14, 2022

  1. refactor: make json script work with gsutil

    @mihirsamdarshi
    mihirsamdarshi committed Aug 14, 2022
    Configuration menu
    Copy the full SHA
    c9d73bb View commit details
    Browse the repository at this point in the history

Commits on Aug 15, 2022

  1. feat: add submit.sh

    @mihirsamdarshi
    mihirsamdarshi committed Aug 15, 2022
    Configuration menu
    Copy the full SHA
    ab78d4c View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2022

  1. feat: add helper delete_json script

    @mihirsamdarshi
    mihirsamdarshi committed Aug 23, 2022
    Configuration menu
    Copy the full SHA
    d1ab897 View commit details
    Browse the repository at this point in the history

Commits on Sep 2, 2022

  1. refactor: run ShellCheck, shellfmt, and pylint on some existing scripts

    @mihirsamdarshi
    mihirsamdarshi committed Sep 2, 2022
    Configuration menu
    Copy the full SHA
    876d8bd View commit details
    Browse the repository at this point in the history

  2. feat: add new helper scripts

    @mihirsamdarshi
    mihirsamdarshi committed Sep 2, 2022
    Configuration menu
    Copy the full SHA
    bc60a69 View commit details
    Browse the repository at this point in the history

  3. feat: refactor status script

    @mihirsamdarshi
    mihirsamdarshi committed Sep 2, 2022
    Configuration menu
    Copy the full SHA
    4adc1e0 View commit details
    Browse the repository at this point in the history

Commits on Sep 3, 2022

  1. feat: continue working on various helper scripts

    @mihirsamdarshi
    mihirsamdarshi committed Sep 3, 2022
    Configuration menu
    Copy the full SHA
    06b6392 View commit details
    Browse the repository at this point in the history

Commits on Sep 7, 2022

  1. fix: mo' problems, mo' fixes

    @mihirsamdarshi
    mihirsamdarshi committed Sep 7, 2022
    Configuration menu
    Copy the full SHA
    55549c5 View commit details
    Browse the repository at this point in the history

Commits on Sep 20, 2022

  1. feat: add in merge_atac_qc_human.R script, fix some parallel processi… 

    …ng, add progress
    @mihirsamdarshi
    mihirsamdarshi committed Sep 20, 2022
    Configuration menu
    Copy the full SHA
    f952b43 View commit details
    Browse the repository at this point in the history

  2. fix: a couple minor script tweaks

    @mihirsamdarshi
    mihirsamdarshi committed Sep 20, 2022
    Configuration menu
    Copy the full SHA
    7a4643f View commit details
    Browse the repository at this point in the history

  3. feat: add in complete wrapper and server setup scripts

    @mihirsamdarshi
    mihirsamdarshi committed Sep 20, 2022
    Configuration menu
    Copy the full SHA
    3220555 View commit details
    Browse the repository at this point in the history

  4. feat: fix wrapper script with better outputs

    @mihirsamdarshi
    mihirsamdarshi committed Sep 20, 2022
    Configuration menu
    Copy the full SHA
    f1c2521 View commit details
    Browse the repository at this point in the history

Commits on Sep 21, 2022

  1. fix: add in fixes for the setup and wrapper scripts

    @mihirsamdarshi
    mihirsamdarshi committed Sep 21, 2022
    Configuration menu
    Copy the full SHA
    576d7c5 View commit details
    Browse the repository at this point in the history

Commits on Oct 14, 2022

  1. feat: update batch scripts

    @mihirsamdarshi
    mihirsamdarshi committed Oct 14, 2022
    Configuration menu
    Copy the full SHA
    4313e4e View commit details
    Browse the repository at this point in the history

  2. feat: add R, fish, neovim, and qc2tsv install to server setup

    @mihirsamdarshi
    mihirsamdarshi committed Oct 14, 2022
    Configuration menu
    Copy the full SHA
    43a8e9e View commit details
    Browse the repository at this point in the history

  3. feat: clean up scripts

    @mihirsamdarshi
    mihirsamdarshi committed Oct 14, 2022
    Configuration menu
    Copy the full SHA
    5a938f4 View commit details
    Browse the repository at this point in the history

Commits on Oct 17, 2022

  1. feat: clean up scripts

    @mihirsamdarshi
    mihirsamdarshi committed Oct 17, 2022
    1 Configuration menu
    Copy the full SHA
    4661741 View commit details
    Browse the repository at this point in the history

Commits on Jan 20, 2023

  1. fix: add samtools quickcheck

    @mihirsamdarshi
    mihirsamdarshi committed Jan 20, 2023
    Configuration menu
    Copy the full SHA
    546d195 View commit details
    Browse the repository at this point in the history

Commits on Feb 24, 2023

  1. fix: use date for job log

    @mihirsamdarshi
    mihirsamdarshi committed Feb 24, 2023
    Configuration menu
    Copy the full SHA
    d38e89e View commit details
    Browse the repository at this point in the history

  2. fix: update echo command make_json_singleton.sh

    @mihirsamdarshi
    mihirsamdarshi committed Feb 24, 2023
    Configuration menu
    Copy the full SHA
    1184b1d View commit details
    Browse the repository at this point in the history

  3. feat: clean up src directory, get ready for submission

    @mihirsamdarshi
    mihirsamdarshi committed Feb 24, 2023
    Configuration menu
    Copy the full SHA
    2930dcf View commit details
    Browse the repository at this point in the history

  4. chore: add latest updates to README.md

    @mihirsamdarshi
    mihirsamdarshi committed Feb 24, 2023
    Configuration menu
    Copy the full SHA
    a541e42 View commit details
    Browse the repository at this point in the history

  5. feat: add --bar to all GNU parallel jobs

    @mihirsamdarshi
    mihirsamdarshi committed Feb 24, 2023
    Configuration menu
    Copy the full SHA
    b1344c4 View commit details
    Browse the repository at this point in the history

Commits on Mar 3, 2023

  1. Added scripts used to process pass1ac data. Made minor changes to scr… 

    …ipt to match consistent naming convention for pass data
    @archanaraja
    archanaraja committed Mar 3, 2023
    Configuration menu
    Copy the full SHA
    94038c5 View commit details
    Browse the repository at this point in the history

Commits on Mar 6, 2023

  1. fix: fix shebang in server setup script

    @mihirsamdarshi
    mihirsamdarshi committed Mar 6, 2023
    Configuration menu
    Copy the full SHA
    8fe1aa4 View commit details
    Browse the repository at this point in the history

Commits on Mar 7, 2023

  1. chore: add merge_jsons.py utility script

    @mihirsamdarshi
    mihirsamdarshi committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    cef9d4c View commit details
    Browse the repository at this point in the history

  2. fix: remove trailing slash from input dir

    @mihirsamdarshi
    mihirsamdarshi committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    9dc3e53 View commit details
    Browse the repository at this point in the history

Commits on Mar 8, 2023

  1. fix: point to correct script names in wrappers

    @mihirsamdarshi
    mihirsamdarshi committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    944b310 View commit details
    Browse the repository at this point in the history

  2. fix: remove home dir path addition from wrapper script

    @mihirsamdarshi
    mihirsamdarshi committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    19ab3ef View commit details
    Browse the repository at this point in the history

  3. fix: fix paths in scripts

    @mihirsamdarshi
    mihirsamdarshi committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    5940239 View commit details
    Browse the repository at this point in the history

Commits on Mar 11, 2023

  1. Fix : remove printing out encode workflow level qc , added vial_label… 

    … column
    @archanaraja
    archanaraja committed Mar 11, 2023
    Configuration menu
    Copy the full SHA
    64c80ab View commit details
    Browse the repository at this point in the history

Commits on Mar 21, 2023

  1. fix: fix paths in scripts

    @mihirsamdarshi
    mihirsamdarshi committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    6d645d8 View commit details
    Browse the repository at this point in the history

Commits on Apr 1, 2024

  1. Merge branch 'master' into ms-patch-1

    @mihirsamdarshi
    mihirsamdarshi authored Apr 1, 2024
    Configuration menu
    Copy the full SHA
    1238134 View commit details
    Browse the repository at this point in the history