Update README.md

README.md

@@ -6,24 +6,31 @@ params: Input arguments required by the stage.
 
 *Commands*
 - stage: all (TransSynW + PAGA + SIGNET + TRRUST + Cytoscape + Uniprot)
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 Eg: python main.py run all --artefacts ./artefacts/temp2 --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES ./Signet/terminal.csv ./trrust_rawdata_human.tsv
 
 - stage: mechanistic insights (TransSynW + PAGA)
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 Eg: python main.py run mechanistic_insights --artefacts ./artefacts/temp2 --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES
 
 - stage: grn inference (SIGNET)
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 Eg: python main.py run grn_inference --artefacts ./artefacts/temp --params ./Signet/terminal.csv
 
 - stage: functional analysis (Uniprot)
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 Eg: python main.py run functional_analysis --artefacts ./artefacts/Results-2023-10-03_12-39-19
 
 - stage: gene network (Cytoscape)
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 Eg: python main.py run generate_network --artefacts ./artefacts/Results-2023-10-03_12-39-19 --params ./artefacts/Results-2023-10-03_12-39-19/trrust_analysis.csv
 
 - stage: trrust analysis (TRRUST)
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 Eg: python main.py run trrust_analysis --artefacts ./artefacts/Results-2023-10-03_12-39-19 --params ./trrust_rawdata_human.tsv 
 
 - stage: generate_hypothesis (TransSynW)
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 Eg: python main.py run generate_hypothesis --artefacts ./artefacts/temp2 --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES
 python main.py run generate_hypothesis --artefacts ${PWD}/artefacts/temp2 --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES