Main SLUPipe Commands
Activate Anaconda Environment
$ source activate SLUPipe
Execute Pipeline Workflow
$ python3 slupipe.py <config.json>
Version Summary & Execution Description
$ python3 slupipe.py
Check Latest Software Release
$ python3 slupipe.py --update
Run SLUPipe With Custom Variant Caller Configurations
$ python3 slupipe.py <config.json> <muse.json> <mutect.json>
Run SLUPipe In HPC Mode
- Generate Batches
$ python3 gen_batches.py <base_configuration_file> - Run Bash Script
$ ./run_slupipe_hpc.sh
Example Workflow
Pipeline Workflow Example (Non-paired Mode):
(SLUPipe)$ python3 slupipe.py config.json
TUMOR MODE: DIRECTORY SUMMARY (X to Exit):
--------------------------------------------------------------------------------
NO. ID TUMOR
--------------------------------------------------------------------------------
1 tumor2_T tumor2_T.bam
2 tumor1_T tumor1_T.bam
IS THIS CORRECT (Y/N): Y
SELECT FILE NUMBERS TO PROCESS (Separate File Numbers By Space): 1
############################
COMMENCING PIPELINE WORKFLOW
############################
Pindel: Calling Variants -> tumor2_T
Pindel: Calling Variants Complete -> tumor2_T
Platypus: Calling Variants -> tumor2_T
Platypus: Calling Variants Complete -> tumor2_T
MuTect2: Calling Variants -> tumor2_T
Mutect2: Calling Variants Complete -> tumor2_T
Ensembl VEP: Annotating Variants -> tumor2_T-pindel
Ensembl VEP: Annotating Variants Complete -> tumor2_T-pindel
Ensembl VEP: Annotating Variants -> tumor2_T-platypus
Ensembl VEP: Annotating Variants Complete -> tumor2_T-platypus
Ensembl VEP: Annotating Variants -> tumor2_T-mutect2
Ensembl VEP: Annotating Variants Complete -> tumor2_T-mutect2
VCF2MAF: Converting VCF to MAF -> tumor2_T-pindel
VCF2MAF: VCF to MAF Conversion Complete -> tumor2_T-pindel
VCF2MAF: Converting VCF to MAF -> tumor2_T-platypus
VCF2MAF: VCF to MAF Conversion Complete -> tumor2_T-platypus
VCF2MAF: Converting VCF to MAF -> tumor2_T-mutect2
VCF2MAF: VCF to MAF Conversion Complete -> tumor2_T-mutect2
Merging MAF: Saving Merged MAFs -> ./output/maf/tumor2_T.final.maf
---------------------- MERGED MAF SUMMARY ---------------------------
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 1619 entries, 0 to 1618
Columns: 134 entries, Hugo_Symbol to variant_caller
dtypes: float64(70), int64(5), object(59)
memory usage: 1.7+ MB
None
count 1619
unique 1
top maf
freq 1619
Name: variant_caller, dtype: object
---------------------------------------------------------------------
############################
PIPELINE WORKFLOW COMPLETE
############################