update help for --step

main.nf

@@ -27,9 +27,20 @@
 
      Options:
      
-       --step                        Choose one step into: "01_clean_qc", "02_assembly", "03_filtering", "04_structural_annot", "05_alignment", "06_func_annot", "07_taxo_affi", "08_binning".
-                                     Only exception: "03_filtering" step can be associated with coma to "04_structural_annot", "05_alignment", "06_func_annot", "07_taxo_affi" and "08_binning".
-
+       --step                        Choose step(s) into: "01_clean_qc", "02_assembly", "03_filtering",
+                                     "04_structural_annot", "05_alignment", "06_func_annot", "07_taxo_affi", "08_binning".
+                                     i. You can directly indicate the final step that is important to you. For example,
+                                     if you are interested in binning (and the taxonomic affiliation of bins), just use --step "08_binning".
+                                     It runs the previous steps automatically (except "03_filtering", see ii).
+                                     ii. "03_filtering" is automatically skipped for the next steps
+                                     "04_structural_annot", "05_alignment", "06_func_annot", "07_taxo_affi" and "08_binning".
+                                     If you want to filter your assembly before doing one of these steps, you must use --step "03_filtering,the_step",
+                                     for example --step "03_filtering,04_structural_annot".
+                                     iii. When you run one of the three steps "06_func_annot", "07_taxo_affi" or "08_binning" during a first analysis
+                                     and then another of these steps interests you and you run metagWGS again to get the result of this other step,
+                                     you have to indicate --step "the_first_step,the_second_step". This will allow you to have a final MultiQC html report
+                                     that will take into account the metrics of both analyses performed. If the third of these steps interests you and you run again
+                                     metagWGS for this step, you also have to indicate --step "the_first_step,the_second_step,the_third,step" for the same reasons.
      01_clean_qc options:
        --skip_01_clean_qc            Skip 01_clean_qc step.
        --adapter1                    Sequence of adapter 1. Default: Illumina TruSeq adapter.