rplaced download with ena

modules/local/ena.nf

@@ -1,31 +1,32 @@
 process ENA_DOWNLOAD {
     tag           "${SRR}"
     label         "process_single"
-    container     'staphb/viridian:1.3.0'
+    container     'staphb/enabrowsertools:1.7.1'
 
     input:
     val(SRR)
 
     output:
-    tuple val(SRR), file("reads/${SRR}_{1,2}.fastq.gz"), emit: fastq
+    tuple val(SRR), file("*/*{1,2}.fastq.gz"), emit: fastq, optional: true
     path "logs/*/*.log", emit: log
     path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${SRR}"
     """
     mkdir -p reads logs/${task.process}
-    log_file=logs/${task.process}/${SRR}.${workflow.sessionId}.log
+    log_file=logs/${task.process}/${prefix}.${workflow.sessionId}.log
 
     enaDataGet \
+        ${args} \
         -f fastq \
         ${SRR} \
         | tee -a \$log_file
 
-    mv */*fastq.gz reads/.
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         enaDataGet: \$( enaDataGet -v | awk '{print \$NF}' )