Merge pull request #75 from EBI-Metagenomics/fix/readme-fix-links

Update README.md: fix dead links to download files

README.md

@@ -75,7 +75,7 @@ cd containers && bash build.sh
 
 ## Data preparation
 
-1. You need to pre-download your data to directories and make sure that genomes are uncompressed. Scripts to fetch genomes from ENA ([fetch_ena.py](https://github.com/EBI-Metagenomics/genomes-pipeline/blob/master/containers/genomes-catalog-update/scripts/fetch_ena.py)) and NCBI ([fetch_ncbi.py](https://github.com/EBI-Metagenomics/genomes-pipeline/blob/master/containers/genomes-catalog-update/scripts/fetch_ncbi.py)) are provided and need to be executed separately from the pipeline. If you have downloaded genomes from both ENA and NCBI, put them into separate folders.
+1. You need to pre-download your data to directories and make sure that genomes are uncompressed. Scripts to fetch genomes from ENA ([fetch_ena.py](https://github.com/EBI-Metagenomics/genomes-pipeline/blob/master/bin/fetch_ena.py)) and NCBI ([fetch_ncbi.py](https://github.com/EBI-Metagenomics/genomes-pipeline/blob/master/bin/fetch_ncbi.py)) are provided and need to be executed separately from the pipeline. If you have downloaded genomes from both ENA and NCBI, put them into separate folders.
 
 2. When genomes are fetched from ENA using the `fetch_ena.py` script, a CSV file with contamination and completeness statistics is also created in the same directory where genomes are saved to. If you are downloading genomes using a different approach, a CSV file needs to be created manually (each line should be genome accession, % completeness, % contamination). The ENA fetching script also pre-filters genomes to satisfy the QS50 cut-off (QS = % completeness - 5 * % contamination).