Do not require a pipeline-job.sh script for each workflow step.

[xiamaz]

Is your feature request related to a problem? Please describe.
The pipeline-job.sh script is used for submitting snappy workflows against slurm. Currently when creating a new workflow the pipeline-job.sh template is copied into each step and includes certain user-specific commands:

snappy-pipeline/snappy_pipeline/apps/snappy_start_step.py

Line 134 in c86c665

dest_path=os.path.join(dest_dir, FILENAME_PIPELINE_JOB_SH),

This pipeline-job.sh seldom needs to be adapted for individual workflow steps, as it just provides a wrapper for executing the snakemake workflow on a slurm cluster.

Describe the solution you'd like
Rather than copying the pipeline-job.sh to each new workflow folder. Consider adding the project snappy directory as a default location and provide override possibilities.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Associated cubi-tk issue bihealth/cubi-tk#177