HPC snakemake upgrade incompatibility

[skchronicles]

Snakemake Version Incompatibility: REVERT 5.1.3

Changes were made to module load ccbrpipeliner, master and activeDev branch

HPC upgraded the version of snakemake that is loaded when running module load snakemake/3.5.
Previously, snakemake version 5.1.3 was loaded. Now, snakemake version 5.3.0 is loaded.
This is problematic due to the base command we are using. We are using the -T switch which is no longer supported in the newer version.

Adding explicit module load snakemake/5.1.3 statements after module loading python 3.5 to the following files.

• submit_slurm.template
• pipeline_ctrl.sh
• slurm.template
• ccbrpipe.sh

[skchronicles]

Changed implicit loading of snakemake to an explicit module load

module load snakemake/5.1.3

• master (3406443)
• activeDev (606964e)