update RefSeq db build scripts

db-scripts/build-db-refseq.nf

@@ -15,26 +15,47 @@ Channel.fromPath( assemblySummary )
         def strain  = it[8] - 'strain='
 	def status  = it[11].split(' ')[0].toLowerCase()
         if( species.contains( strain ) )
-            return [ it[0], it[5], species, status, it[19] - 'ftp://ftp.ncbi.nlm.nih.gov/genomes/' ]
+            return [ it[0], it[5], species, status, it[19] - 'https://ftp.ncbi.nlm.nih.gov/genomes/' ]
         else
-            return [ it[0], it[5], "${species} ${strain}", status, it[19] - 'ftp://ftp.ncbi.nlm.nih.gov/genomes/' ]
+            return [ it[0], it[5], "${species} ${strain}", status, it[19] - 'https://ftp.ncbi.nlm.nih.gov/genomes/' ]
     } )
-    .set { validGenomes }
+    .set { chValidGenomes }
+
+
+process download {
+
+    tag { "${acc} - ${orgName}" }
+
+    maxForks 5
+    errorStrategy 'ignore'
+    maxRetries 3
+
+    input:
+    tuple val(acc), val(taxId), val(orgName), val(status), val(path) from chValidGenomes
+
+    output:
+    tuple val(acc), val(taxId), val(orgName), val(status), path("${acc}.gz") into chDownloadedGenomes
+
+    script:
+    """
+    wget -O ${acc}.gz ${ncbiPath}/${path}/${path.split('/').last()}_genomic.fna.gz
+    """
+}
 
 
 process sketch {
 
     tag { "${acc} - ${orgName}" }
 
-    maxForks 4
     errorStrategy 'ignore'
     maxRetries 3
+    conda 'mash=2.3'
 
     input:
-    set val(acc), val(taxId), val(orgName), val(status), val(path) from validGenomes
+    tuple val(acc), val(taxId), val(orgName), val(status), path("${acc}.gz") from chDownloadedGenomes
 
     output:
-    set val(acc), val(taxId), val(status), val(orgName) into dbEntries
+    tuple val(acc), val(taxId), val(status), val(orgName) into chDbEntries
     file("${acc}.msh") into outMash
     file("${acc}.fna.gz") into outFasta
 
@@ -43,14 +64,13 @@ process sketch {
 
     script:
     """
-    wget -O ${acc}.gz ${ncbiPath}/${path}/${path.split('/').last()}_genomic.fna.gz
-    gunzip ${acc}.gz
-    ${REFERENCE_SEEKER_HOME}/share/mash sketch -k 32 -s 10000 ${acc}
+    gunzip -c ${acc}.gz > ${acc}
+    mash sketch -k 32 -s 10000 ${acc}
     mv ${acc} ${acc}.fna
     gzip ${acc}.fna
     """
 }
 
 
-dbEntries.map { "${it[0]}\t${it[1]}\t${it[2]}\t${it[3]}" }
+chDbEntries.map { "${it[0]}\t${it[1]}\t${it[2]}\t${it[3]}" }
     .collectFile( name: 'db.tsv', storeDir: "./${domain}-refseq/", newLine: true )

db-scripts/build-db-refseq.sh

@@ -1,5 +1,5 @@
 
-NCBI_PATH='ftp://ftp.ncbi.nlm.nih.gov/genomes'
+NCBI_PATH='https://ftp.ncbi.nlm.nih.gov/genomes'
 
 DOMAIN=''
 getopts "bavfp" opt;