Panelapp gene query script added

[g-pyxl]

Simple script to generate CSV containing all current gene/panel relations using PanelApp API.
Updated README.

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This change is 

[RachelDuffin]

Suggestion to add a settings.json file - e.g. https://github.com/moka-guys/oncodeep_upload/blob/main/settings.json
This means the same formatting will be applied in vscode as in other existing team projects, to tidy up the scripts

Reviewed 4 of 4 files at r1, all commit messages.
Reviewable status: all files reviewed, 4 unresolved discussions (waiting on @g-pyxl)

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okd_qc_commands.py line 11 at r1 (raw file):

Usage:
    python3 qcgen.py -p {dnanexus_project_id} -f {illumina_runfolder_name}

could you update the script name?

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okd_qc_commands.py line 78 at r1 (raw file):

                # Write the FastQC command for each pair of fastq files
                script_file.write(

You could use f strings here, which can make the code easier to follow

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okd_qc_commands.py line 133 at r1 (raw file):

    
    # Read the DNAnexus auth token from file
    auth_token = read_auth_token("/usr/local/src/mokaguys/.dnanexus_auth_token")

Suggestion to add this as a command line arg instead of the path to the secret

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README.md line 73 at r1 (raw file):

### Usage:

python3 qcgen.py -p {dnanexus_project_id} -f {illumina_runfolder_name}

Could you update the script name here

[g-pyxl]

Added to repo.

Reviewable status: 1 of 6 files reviewed, 4 unresolved discussions (waiting on @RachelDuffin)

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README.md line 73 at r1 (raw file):

Previously, RachelDuffin wrote…

Could you update the script name here

Done.

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okd_qc_commands.py line 11 at r1 (raw file):

Previously, RachelDuffin wrote…

could you update the script name?

Done.

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okd_qc_commands.py line 78 at r1 (raw file):

Previously, RachelDuffin wrote…

You could use f strings here, which can make the code easier to follow

Done, temporarily removing script until genomics server is live

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okd_qc_commands.py line 133 at r1 (raw file):

Previously, RachelDuffin wrote…

Suggestion to add this as a command line arg instead of the path to the secret

Done, temporarily removing script until genomics server is live

[RachelDuffin]

Reviewed 4 of 5 files at r2.
Reviewable status: 5 of 6 files reviewed, all discussions resolved

[RachelDuffin]

Reviewable status: 5 of 6 files reviewed, all discussions resolved

[RachelDuffin]

Reviewed 1 of 5 files at r2, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @g-pyxl)