diff --git a/dataload/nextflow/load_subgraph.nf b/dataload/nextflow/load_subgraph.nf index 5736f23..39b3f74 100644 --- a/dataload/nextflow/load_subgraph.nf +++ b/dataload/nextflow/load_subgraph.nf @@ -451,7 +451,7 @@ process run_materialised_queries { path(neo_db) output: - path("materialised_queries") + path("materialised_queries/*") script: """ @@ -636,8 +636,8 @@ process copy_neo_to_ftp { """ #!/usr/bin/env bash set -Eeuo pipefail - mkdir -p /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()} - cp -f neo4j.tgz /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()}/${params.subgraph}_neo4j.tgz + mkdir -p /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()} + cp -f neo4j.tgz /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()}/${params.subgraph}_neo4j.tgz """ } @@ -655,8 +655,8 @@ process copy_summary_to_ftp { """ #!/usr/bin/env bash set -Eeuo pipefail - mkdir -p /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()} - cp -f ${summary_json} /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()}/ + mkdir -p /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()} + cp -f ${summary_json} /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()}/ """ } @@ -674,8 +674,8 @@ process copy_solr_to_ftp { """ #!/usr/bin/env bash set -Eeuo pipefail - mkdir -p /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()} - cp -f solr.tgz /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()}/${params.subgraph}_solr.tgz + mkdir -p /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()} + cp -f solr.tgz /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()}/${params.subgraph}_solr.tgz """ } @@ -693,8 +693,8 @@ process copy_sqlite_to_ftp { """ #!/usr/bin/env bash set -Eeuo pipefail - mkdir -p /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()} - cp -f ${params.subgraph}.sqlite3 /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()}/${params.subgraph}.sqlite3 + mkdir -p /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()} + cp -f ${params.subgraph}.sqlite3 /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()}/${params.subgraph}.sqlite3 """ } @@ -713,8 +713,9 @@ process copy_mat_queries_to_ftp { """ #!/usr/bin/env bash set -Eeuo pipefail - mkdir -p /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()} - cp -f ${csvs} ${sqlite} /nfs/ftp/public/databases/spot/kg/${params.config}/${params.timestamp.trim()}/ + mkdir -p /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()}/query_results + cp -f ${csvs} /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()}/query_results/ + cp -f ${sqlite} /nfs/ftp/public/databases/spot/kg/${params.subgraph}/${params.timestamp.trim()}/query_results/all_query_results.sqlite3.gz """ } diff --git a/dataload/scripts/dataload_codon.sh b/dataload/scripts/dataload_codon.sh index ac2426f..202c687 100755 --- a/dataload/scripts/dataload_codon.sh +++ b/dataload/scripts/dataload_codon.sh @@ -4,7 +4,7 @@ export GREBI_QUERY_YAMLS_PATH=/nfs/production/parkinso/spot/grebi/materialised_q export GREBI_TMP=/hps/nobackup/parkinso/spot/grebi/tmp export GREBI_CONFIG=ebi export GREBI_IS_EBI=true -export GREBI_TIMESTAMP=$(date +%Y_%m_%d__%H_%M) +export GREBI_TIMESTAMP=$(date +"%Y-%b-%d") export GREBI_MAX_ENTITIES=1000000000 export GREBI_NEXTFLOW_CONFIG=$GREBI_DATALOAD_HOME/nextflow/codon_nextflow.config module load nextflow-22.10.1-gcc-11.2.0-ju5saqw