Strip "chr" prefix for GRCh38

[holtgrewe]

Describe the bug
We currently write out the "chr" prefix for GRCh38 when running cadd-scripts v1.6. This is problematic (see link below).

To Reproduce
Steps to reproduce the behavior:

1. Run a file with chr prefix through CADD.
2. See error from bottom.

Expected behavior
Strip the chr prefix for calling cadd-scripts. Do not forget to add it back when importing. ;-)

Additional context

• CADD 1.6: Encountered uncovered chromosome/Possible precedence issue with control flow operator kircherlab/CADD-scripts#37
• We can just "always" strip the prefix for GRCh37 as well.

Error Logs

+ /opt/miniconda3/share/cadd-scripts-1.6-0/CADD.sh -a -g GRCh38 -v v1.6 -o /tmp/cadd_restyf1v289p/out.tsv.gz /tmp/cadd_restyf1v289p/in.vcf
/bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Job counts:
	count	jobs
	1	annotation
	1	imputation
	1	join
	1	prepare
	1	prescore
	1	score
	6
Opening /opt/miniconda3/share/cadd-scripts-1.6-0/data/prescored/GRCh38_v1.6/incl_anno/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz...
Encountered uncovered chromosome
Possible precedence issue with control flow operator at /opt/miniconda3/share/cadd-scripts-1.6-0/envs/b10f19082a56fe8134c14e0b9593442f/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Input file /tmp/tmp.r77o9qiwV2/in.csv.gz is empty.
[Tue Jan 30 08:16:21 2024]
Error in rule join:
    jobid: 0
    output: /tmp/tmp.r77o9qiwV2/in.tsv.gz
    conda-env: /opt/miniconda3/share/cadd-scripts-1.6-0/envs/b10f19082a56fe8134c14e0b9593442f
    shell:
        
        (
        echo "##CADD GRCh38-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2020. All rights reserved.";
        head -n 1 /tmp/tmp.r77o9qiwV2/in.novel.tsv;
        cat /tmp/tmp.r77o9qiwV2/in.pre.tsv /tmp/tmp.r77o9qiwV2/in.novel.tsv         | grep -v "^#"         | sort -k1,1 -k2,2n -k3,3 -k4,4
        ) | bgzip -c > /tmp/tmp.r77o9qiwV2/in.tsv.gz;
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message

2024-01-30 08:16:23.049409+00:00 | info | ... done running the worker
2024-01-30 08:16:23.050440+00:00 | info | Create result set and import worker results ...