For each of the modules, add a shell script as was done in generate_reference_tables #155
Description
To facilitate understanding of each of the modules, add a shell script that illustrates how this is done in the same manner as was done in the generate_reference_tables module.
Modules missing the shell (if checked - then already done - could be nextflow command):
- 5p_utr_status
- accession_mapping
- cpat
- filter_sqanti
- generate_reference_tables
- isoseq3
- make_gencode_database
- make_hybrid_database
- make_pacbo_cds_gtf. - needs to be made not relative to private directory
- orf_calling
- peptide_analysis
- peptide_novelty_analysis
- protein_classification
- protein_database_aggregate - protein_database_aggregation.py not found in this repository -
- protein_filter
- protein_gene_rename
- protein_groups_compare
- protein_inference
- refine_orf_database
- six_frame_translation
- sqanti3
- transcriptome_summary
- visualization_track