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Ensembl · Aug 2, 2024 · fdda088 · fdda088
1 parent 08cc4f0
commit fdda088
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/pipelines/nextflow/modules/store_into_db.nf b/pipelines/nextflow/modules/store_into_db.nf
@@ -24,7 +24,7 @@ process STORE_INTO_DB {
     scratch false
     label 'default'
     tag "$run_accession"
-    //maxForks 20
+    maxForks 10
 
     input:
     tuple val(taxon_id), val(gca), val(run_accession), val(query)
@@ -58,7 +58,7 @@ process STORE_INTO_DB {
             query = query.trim()
             // Check if the query is not empty
             if (query) {
-                //log.info("queriesArray[${index}] ${query};")
+                log.info("STORE INTO DB  ${query};")
                 setMetaDataRecord(query.toString())
             }
         }

diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf
@@ -22,7 +22,7 @@ process FETCH_GENOME {
 
   //storeDir "${params.outDir}/$taxon_id/$gca/ncbi_dataset/"
   afterScript "sleep $params.files_latency"  // Needed because of file system latency
-  maxForks 1
+  maxForks 10
 
   input:
   tuple val(taxon_id), val(gca), val(run_accession), val(pair1), val(pair2)

diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
@@ -22,7 +22,7 @@ process INDEX_GENOME {
     tag "$taxon_id:$gca"
     publishDir "${params.outDir}/$taxon_id/$gca/ncbi_dataset/", mode: 'copy'
     afterScript "sleep $params.files_latency"  // Needed because of file system latency
-    maxForks 1
+    maxForks 10
 
     input:
     tuple val(taxon_id), val(gca), val(run_accession), val(pair1), val(pair2), val(genomeDir)

diff --git a/pipelines/nextflow/modules/utils.nf b/pipelines/nextflow/modules/utils.nf
@@ -109,7 +109,7 @@ def setLastCheckDate(String taxonId,String query_option) {
 }
 
 def setMetaDataRecord(String mysqlQuery){
-    synchronized(this) {
+  //  synchronized(this) {
     def sql 
     sql = Sql.newInstance(jdbcUrl, params.transcriptomic_dbuser,params.transcriptomic_dbpassword,driver)
 
@@ -156,7 +156,7 @@ def setMetaDataRecord(String mysqlQuery){
     }
 }
 }
-}
+//}
 
 
 def getDataFromTable(String queryKey, String queryTable, String tableColumn, String tableValue){