All metadata API responses will have the form
{
"data": "content of the response",
"message": "Description of what happened"
}Following responses and definitions will only show the expected value of the data field
Definition
GET /fetchmetadata
-run_accession : sequence reads accession
-top:: Top n species with best fraction total reads coverage per hits (run_accession)
Arguments
{
{"run_accession": ["ERR4025298|ERR4025300|ERR4025297|ERR4025298"],"top":"1" }
}Response
200 OKon success
{
"data": [
{
"added_reads": 26070,
"fraction_total_reads": 0.99863,
"kraken_assigned_reads": 1097463,
"name": "Salmonella enterica",
"new_est_reads": 1123533,
"run_accession": "ERR4025297",
"taxonomy_id": 28901
},
{
"added_reads": 24518,
"fraction_total_reads": 0.98853,
"kraken_assigned_reads": 1293161,
"name": "Salmonella enterica",
"new_est_reads": 1317679,
"run_accession": "ERR4025298",
"taxonomy_id": 28901
},
{
"added_reads": 22059,
"fraction_total_reads": 0.99077,
"kraken_assigned_reads": 1191343,
"name": "Salmonella enterica",
"new_est_reads": 1213402,
"run_accession": "ERR4025300",
"taxonomy_id": 28901
}
]
}404Not found
{
"message": "run accession not found",
"data": {}
}database/ena_bracken.sql.gz
Code forked from https://github.com/EBI-COMMUNITY/ebi-glue/tree/master/BIGSI_FULL
Refer to README for pipeline mode of action.
nextflow run ret_reads.nf -resume -with-report ret_reads_nextflow.html -with-trace ret_trace.txt -with-dag ret_reads_flowchart.png -with-timeline ret_reads_timeline.htmt
nextflow run process_reads_nobloom.nf -resume -with-report process_reads_nextflow.html -with-trace process_trace.txt -with-dag process_reads_flowchart.png -with-timeline process_reads_timeline.html
nextflow run reads_2_CleanCortex.nf -resume -with-report reads_2_CleanCortex_nextflow.html -with-trace reads_2_CleanCortex_trace.txt -with-dag reads_2_CleanCortex_flowchart.png -with-timeline reads_2_CleanCortex_timeline.html