Update docker settings for vcf pipeline

[spcspin]

I update several settings to let the vcf pipeline share the same docker container with RNA pipeline. The update is in the update_docker branch. @amcooksey , could you check if the new Docker settings are compatible with SCINet? Also, @g8tor , could you help me with the code review? Thank you both for your help.

The changes are below:

1. Change apt-get to apt and add --no-install-recommends flag
2. Update tools' version and add tools in Dockerfile: a. update openjdk to 17 b. add cwl runner (cwltool) c. add tabix for indexing vcf file d. add several prerequisites for regtools, including:
   • gfortran, libreadline-dev, libpcre3-dev, build-essential, and libnss-sss e. update samtools to 1.17 f. update sratoolkit to 3.0.2 g. add bwa
3. Remove the compressed file after installing the tools in Dockerfile.
4. Setting the tools let can be accessed directly from the shell: a. gatk b. FastQC c. picard d. trimmomatic
5. Update tools in setup.py file, including: a. update FastQC to v0.12.1 b. update Trimmomatic to 0.39 c. update picard to 3.0.0 d. updaate gatk to 4.4.0.0
6. Update the tools version in utils.py

[amcooksey]

@mpoelchau I built the updated Docker image, pulled it to my directory on CERES and ran an RNAseq test with saceub. No problems.

[mpoelchau]

Thank you @amcooksey !