Partial-runs.md

@@ -32,4 +32,23 @@ python ~/anaconda3/envs/mosca/share/MOSCA/scripts/annotation.py -i {output}/Asse
 ```
 upimapi.py -i {output}/Annotation/{sample}/aligned.blast -o {output}/Annotation/uniprotinfo --blast --full-id
 ```
-7. 
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+7. Run reCOGnizer for each sample
+```
+recognizer.py -f {output}/Annotation/{sample}/fgs.faa -t {threads} -o {output}/Annotation/{sample} -rd {path/to/resources_directory} --remove-spaces
+```
+8. Run quantification, all at once
+```
+python ~/anaconda3/envs/mosca/share/MOSCA/scripts/quantification_analyser.py -e {path/to/experiments_file} -t {threads} -o {output} -if {input_format_of_experiments_file ("excel" or "tsv")}
+```
+9. Join all information
+```
+python ~/anaconda3/envs/mosca/share/MOSCA/scripts/join_information.py -e {path/to/experiments_file} -t {threads} -o {output} -if {input_format_of_experiments_file ("excel" or "tsv")} -nm {normalization_method ("TMM" or "RLE"}
+```
+10. Run KEGGCharter
+```
+kegg_charter.py -f {output}/MOSCA_Entry_Report.xlsx -o {output}/KEGG_maps -mm {metabolic_maps comma-separate (e.g. 00030,00680,...)} -gcol {mg_names comma-separated} -tcol {mt_names comma-separated} -tc 'Taxonomic lineage ({taxa_level})' -not {number_of_taxa} -keggc 'Cross-reference (KEGG)'
+```
+11. Run final reporting
+```
+python ~/anaconda3/envs/mosca/share/MOSCA/scripts/report.py -e {path/to/experiments_file} -o {output} -ldir ~/anaconda3/envs/mosca/share/MOSCA/resources -if {input_format_of_experiments_file ("excel" or "tsv")}
+```
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