diff --git a/pipelines/nextflow/modules/store_into_db.nf b/pipelines/nextflow/modules/store_into_db.nf index 0da902c..3181bfa 100644 --- 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 ${query};") setMetaDataRecord(query.toString()) } } diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf index 3515f38..9ab99f0 100644 --- a/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf +++ b/pipelines/nextflow/modules/transcriptomic_alignment/fetch_genome.nf @@ -22,7 +22,7 @@ process FETCH_GENOME { //storeDir "${params.outDir}/$taxon_id/$gca/ncbi_dataset/" afterScript "sleep $params.files_latency" // Needed because of file system latency - maxForks 1 + maxForks 10 input: tuple val(taxon_id), val(gca), val(run_accession), val(pair1), val(pair2) diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf index 5e0c908..c260a84 100644 --- a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf +++ b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf @@ -22,7 +22,7 @@ process INDEX_GENOME { tag "$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 index dce471c..a539fb1 100644 --- 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){