Merge 398f52b into d142b57

nextflow/EVAImport/main.nf

@@ -0,0 +1,130 @@
+/* 
+ * Nextflow pipeline to import variants from EVA
+ */
+
+nextflow.enable.dsl=2
+nextflow.enable.strict = true
+
+// Scripts
+eva_script     = "${ENSEMBL_ROOT_DIR}/ensembl-variation/scripts/import/import_vcf.pl"
+var_syn_script = "${ENSEMBL_ROOT_DIR}/ensembl-variation/scripts/import/import_variant_synonyms"
+
+// Common params
+//params.help            = false
+params.species         = null
+params.release         = null
+params.registry        = null
+
+// Params for EVA import script
+params.input_file      = null
+params.source          = "EVA"
+params.description     = "Short variant data imported from EVA"
+params.version         = 4
+params.remove_prefix   = false
+params.chr_synonyms    = false
+params.merge_all_types = true
+params.fork            = 10
+params.skip_tables     = "allele,allele_code,population,population_genotype,genotype_code,compressed_genotype_var,sample"
+params.output_file     = null
+params.sort_vf         = true
+
+// Params for variant synonyms import
+params.var_syn_file    = null
+params.host            = ""
+params.port            = ""
+params.dbname          = ""
+
+
+// Check input params
+if(!params.species) {
+  exit 1, "ERROR: species name must be provided when running EVA import"
+}
+
+if(!params.input_file || !file(params.input_file)) {
+  exit 1, "ERROR: a valid input file must be provided when running EVA import"
+}
+
+if(!params.release || !params.registry) {
+  exit 1, "ERROR: release version and registry file must be provided when running EVA import"
+}
+
+if( (!params.host || !params.port || !params.dbname) && params.species == "rattus_norvegicus") {
+  exit 1, "ERROR: please provide a host, port and db name for a previous rat database"
+}
+
+
+// Build command to run EVA import
+command_to_run = " -i ${params.input_file} --source ${params.source} --source_description '${params.description}' --version ${params.version} --registry ${params.registry} --species ${params.species} --skip_tables '${params.skip_tables}'"
+
+
+log.info """
+  Import EVA script: ${eva_script} \
+  Options: ${command_to_run}
+"""
+
+
+process run_eva {
+  input:
+  path eva_script
+  val options
+  val merge_all_types
+  val fork
+  val sort_vf
+  val chr_synonyms
+  val remove_prefix
+  val output_file
+
+  output:
+
+  script:
+  def sort_vf_table     = sort_vf ? " --sort_vf" : ""
+  def merge_all         = merge_all_types ? " --merge_all_types" : ""
+  def use_fork          = fork ? "--fork ${fork}" : ""
+  def chr_synonyms_file = chr_synonyms ? " --chr_synonyms ${chr_synonyms}" : ""
+  def rm_prefix         = remove_prefix ? " --remove_prefix ${remove_prefix}" : ""
+
+  """
+  perl ${eva_script} ${options} $sort_vf_table $merge_all $use_fork $chr_synonyms_file $rm_prefix --output_file ${output_file}
+  """
+}
+
+process run_variant_synonyms {
+  input:
+  path var_syn_script
+  val source_name
+  val species
+  val input_file
+  val registry
+  val host
+  val port
+  val dbname
+
+  output:
+
+  script:
+
+  if(species == "sus_scrofa")
+      """
+        perl ${var_syn_script} --source_name ${source_name} --species ${species} --data_file ${input_file} --registry ${registry}
+        perl ${var_syn_script} --source_name "pig_chip" --species ${species} --registry ${registry}
+      """
+
+  else if(species == "rattus_norvegicus")
+      """
+        perl ${var_syn_script} --source_name ${source_name} --species ${species} --data_file ${input_file} --registry ${registry}
+        perl ${var_syn_script} --source_name "rat" --species ${species} --registry ${registry} --host ${host} --port ${port} --user 'ensro' --db_name $dbname
+      """
+  else 
+      """
+        perl ${var_syn_script} --source_name ${source_name} --species ${species} --data_file ${input_file} --registry ${registry}
+      """
+}
+
+
+workflow {
+  // TODO: run script to truncate tables
+
+  run_eva(file(eva_script), command_to_run, params.merge_all_types, params.fork, params.sort_vf, params.chr_synonyms, params.remove_prefix, params.output_file)
+  run_variant_synonyms(file(var_syn_script), params.source, params.species, params.var_syn_file, params.registry, params.host, params.port, params.dbname)
+
+}

nextflow/EVAImport/nextflow.config

@@ -0,0 +1,37 @@
+profiles {
+  standard { 
+    process.executor = 'local'
+    process.memory = '2GB'
+    process.cpus = 1
+  }
+
+  lsf {
+    process.executor = 'lsf'
+    process.memory = '2GB'
+    process.cpus = 1
+    process.clusterOptions = '-R "select[mem>2000] rusage[mem=2000]" -M2000'
+  }
+}
+
+process {
+  queue  = 'production'
+  memory = '2 GB'
+}
+
+dag {
+    enabled = true
+    overwrite = true
+    file = "reports/flowchart.html"
+}
+
+timeline {
+    enabled = true
+    overwrite = true
+    file = "reports/timeline.html"
+}
+
+report {
+    enabled = true
+    overwrite = true
+    file = "reports/report.html"
+}