check if genome file has not been downloaded

Ensembl · Aug 14, 2024 · e81462f · e81462f
1 parent ad46333
commit e81462f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf
@@ -33,7 +33,7 @@ process FETCH_GENOME {
 
   script:
   """
-  if [ ! -d "${params.outDir}/${taxon_id}/${gca}/ncbi_dataset/" ]; then
+  if [ ! -d "${params.outDir}/${taxon_id}/${gca}/ncbi_dataset/"  ]  ||  [ ! -n "\$(find "\${params.outDir}/${taxon_id}/${gca}/ncbi_dataset/" -type f -name '*.fna' 2>/dev/null)" ]; then
     echo "Directory ncbi_dataset does not exist. Proceeding with download..."
     curl --retry 3  -X GET "${params.ncbiBaseUrl}/${gca}/download?include_annotation_type=GENOME_FASTA&hydrated=FULLY_HYDRATED" -H "Accept: application/zip" --output genome_file.zip
     unzip -j genome_file.zip