update readme

README.md

@@ -14,32 +14,29 @@ Scripts to convert FASTA files into reference database with NCBI taxonomy.
 
 ## Workflow
 
-* inputs:
-    * FASTA file
+![mkbdr](docs/mkbdr.png)
 
 
-1. Check FASTA format
-2. Check species name format
-3. Check DNA sequence format
-4. Check species name against NCBI taxonomy
-5. Attribute NCBI taxid
-6. Write `valid`, `faulty_taxon` and `faulty_format` FASTA files
-7. Curate species name using `curation` CSV file
-8. Write new nodes in NCBI taxonomy for unattributed taxid species
-9. Write `valid` FASTA files
+## Credits
 
-* outputs:
-    * formatted FASTA file
-    * .ldx new nodes for missing taxid into the taxonomy to link to existing genus/family taxid
+**MKBDR** was coded and written by Pierre-Edouard Guerin.
 
+We thank the following people for their help in the development of this software: Virginie Marques, Alice Valentini, David Mouillot, Emilie Boulanger, Laetitia Mathon, Laura Benestan, Stephanie Manel, Tony Dejean.
 
-1. `raw fasta` --> validate --> `valid fasta` `faulty_format fasta` `faulty_taxon fasta`
 
-2. `faulty_taxon fasta` --> curegen --> `curation csv`
 
-3. verifier et corriger à la main le tableau `curation csv`
+## Contributions and Support
+
+:bug: If you are sure you have found a bug, please submit a bug report. You can submit your bug reports on Gitlab [here](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database/-/issues).
+
+
+
+
+For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).
+
+[![Get help on Slack](https://img.shields.io/badge/slack-cefebev%23basereference-4A154B?logo=slack)](https://cefebev.slack.com/archives/C01MDQSS57F)
+
 
-4. `raw fasta` `curation csv` --> validate --> `valid fasta` et mise à jour de la taxonomy
 
 
 ## Environment
@@ -120,6 +117,8 @@ python3 mkbdr validate --fasta teleo_ok.fasta --curate curated_taxon.csv --outpu
 cd TAXO/testouille; tar zxvf taxdump_2021.tar.gz ; cd ../../
 python3 mkbdr validate --fasta teleo_ok.fasta --curate curated_taxon.csv --output_prefix "truc" --curate curated_taxon.csv --ncbi_taxdump TAXO/testouille --ncbi_taxdump_edition
 ```
+mkbdr validate --fasta teleo_ok.fasta --curate curated_taxon.csv --output_prefix "laetinicer" --ncbi_taxdump_edition --ncbi_taxdump TAXO/testouille
+
 
 obitools
 
@@ -171,4 +170,5 @@ name class				-- (synonym, common name, ...)
 
 wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
 tar zxvf taxdump.tar/gz
-cd TAXO/testouille; tar zxvf taxdump_2021.tar.gz ; cd ../../
\ No newline at end of file
+cd TAXO/testouille; tar zxvf taxdump_2021.tar.gz ; cd ../../
+