explain

Author: bayraktar1

README.md

@@ -9,7 +9,11 @@ snakemake -s workflow/metadata.smk --executor slurm -j 20 --default-resources sl
 snakemake -s workflow/downloads.smk --executor slurm -j 20 --default-resources slurm_account=dla_mm slurm_partition=cpu --keep-going --use-conda --conda-frontend mamba --latency-wait 60 --printshellcmds
 ```
 `Metadata.smk` should NOT be run with `--keep-going`, all rules should always finish without errors. <br>
-`Downloads.smk` should be run with `--keep-going`, because it is possible that the files belonging to a NCBI accession are no longer available which means that the rule for that accession will fail.
+`Downloads.smk` should be run with `--keep-going`, because it is possible that the files belonging to a NCBI accession are no longer available which means that the rule for that accession will fail. Or a sample is invalid and will fail during fasterq-dump.
 
-## Selecting species
-You can specify NCBI taxon ids in `config/metadata.yaml` under `taxon_id`. Single or multiple taxons can be specified separated by a space. **If you specify a taxon id that belongs to a rank higher than a species, all species of that rank will be downloaded!**
+## Selecting species & accessions
+You can specify NCBI taxon ids in `Data/taxons.txt`. Single or multiple taxons can be specified separated by a space. **If you specify a taxon id that belongs to a rank higher than a species, all species of that rank will be downloaded!**
+
+Sample accession and study accession can be specified in `Data/accessions.txt`. All samples associated with a study will be collected and downloaded.
+
+You can combine as long as you specify everything in their respective files.