For each of the modules, add a shell script as was done in generate_reference_tables - Githubissues

sheynkman-lab / Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

MIT License

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For each of the modules, add a shell script as was done in generate_reference_tables #155

Open adeslatt opened 2 years ago

adeslatt commented 2 years ago

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):

[x] 5p_utr_status
[ ] accession_mapping
[x] cpat
[ ] filter_sqanti
[x] generate_reference_tables
[ ] isoseq3
[ ] make_gencode_database
[ ] make_hybrid_database
[x] make_pacbo_cds_gtf. - needs to be made not relative to private directory
[ ] orf_calling
[x] peptide_analysis
[ ] peptide_novelty_analysis
[x] protein_classification
[ ] protein_database_aggregate - protein_database_aggregation.py not found in this repository -
[x] protein_filter
[ ] protein_gene_rename
[x] protein_groups_compare
[ ] protein_inference
[x] refine_orf_database
[ ] six_frame_translation
[x] sqanti3
[x] transcriptome_summary
[x] visualization_track