About run_salmon_spg_wf_on_biowulf …
run_salmon_spg_wf_on_biowulf is a command line python script that runs salmon_spg_wf only or both salmon_spg_wf then quant_sf2express_table (with use of flag –generate_exp_tables ).
Command-line Usage to run salmon_spg_wf only
python run_salmon_spg_wf_on_biowulf.py \
–bill_to org-nci_ccr_so1 \
–invitees mcintoshc, pcf \
–salmon_library project-FXgYz7005FKkPZkbBxbVGXQv:file-FXYq2180v1xq1k4p3g5g99q8 \
–fastq_directory /…/FASTQ \
–with_project A_JUNK_PROJECT \
–name analysis_name
Command-line Usage to run both salmon_spg_wf and quant_sf2express_tables.
python run_salmon_spg_wf_on_biowulf.py \
–bill_to org-nci_ccr_so1 \
–invitees mcintoshc, pcf \
–salmon_library project-FXgYz7005FKkPZkbBxbVGXQv:file-FXYq2180v1xq1k4p3g5g99q8\
–fastq_directory /…/FASTQ \
–with_project A_JUNK_PROJECT \
–generate_exp_tables \
–name analysis_name
Output Files
- Salmon SPG WF output files -see Output Files section with link salmon_spg_wf.
- QuantSF output files -see Output Files section with link quant_sf2express_table.
- Find out more about GAU’s DNAnexus Pilot Program.
- For NCI Members who want to use DNAnexus or develop you must get an account.
Developed by GAU
- Peter FitzGerald (email: fitzgepe@mail.nih.gov)
- Carl McIntosh (email: mcintoshc@mail.nih.gov)