a new function

wtsi-npg · Dec 12, 2018 · 7dfc10a · 7dfc10a
1 parent d52362b
commit 7dfc10a
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diff --git a/Changes b/Changes
@@ -50,6 +50,7 @@ LIST OF CHANGES
    for the rest
  - explicitly use iRODS loader from an 'old' dated directory for
    old style runfolders
+ - a new function, archive_run_data_to_irods, to publish run-level non-product data to iRODS
 
 release 52.1
  - bug fix in jobs names where jobs name should include the pipeline

diff --git a/data/config_files/function_list_central_qc_run.json b/data/config_files/function_list_central_qc_run.json
@@ -171,6 +171,11 @@
             "source" : "run_archival_in_progress",
             "target" : "archive_to_irods_samplesheet"
          },
+         {
+            "relation" : "dependsOn",
+            "target" : "archive_run_data_to_irods",
+            "source" : "archive_to_irods_samplesheet"
+         },
          {
             "relation" : "dependsOn",
             "source" : "archive_to_irods_samplesheet",
@@ -186,6 +191,11 @@
             "source" : "archive_to_irods_samplesheet",
             "target" : "upload_auto_qc_to_qc_database"
          },
+         {
+            "relation" : "dependsOn",
+            "target" : "run_run_archived",
+            "source" : "archive_run_data_to_irods"
+         },
          {
             "relation" : "dependsOn",
             "target" : "run_run_archived",
@@ -321,6 +331,10 @@
             "id" : "archive_to_irods_samplesheet",
             "label" : "archive_to_irods_samplesheet"
          },
+         {
+            "id" : "archive_run_data_to_irods",
+            "label" : "archive_run_data_to_irods"
+         },
          {
             "id" : "run_run_archived",
             "label" : "run_run_archived"

diff --git a/data/config_files/function_list_post_qc_review.json b/data/config_files/function_list_post_qc_review.json
@@ -16,6 +16,11 @@
             "source" : "update_ml_warehouse",
             "target" : "archive_to_irods_ml_warehouse"
          },
+         {
+            "relation" : "dependsOn",
+            "target" : "archive_run_data_to_irods",
+            "source" : "archive_to_irods_ml_warehouse"
+         },
          {
             "relation" : "dependsOn",
             "target" : "upload_fastqcheck_to_qc_database",
@@ -41,6 +46,11 @@
             "target" : "run_run_archived",
             "source" : "upload_illumina_analysis_to_qc_database"
          },
+         {
+            "relation" : "dependsOn",
+            "target" : "run_run_archived",
+            "source" : "archive_run_data_to_irods"
+         },
          {
             "relation" : "dependsOn",
             "target" : "run_run_archived",
@@ -94,6 +104,10 @@
             "id" : "archive_to_irods_ml_warehouse",
             "label" : "archive_to_irods_ml_warehouse"
          },
+         {
+            "id" : "archive_run_data_to_irods",
+            "label" : "archive_run_data_to_irods"
+         },
          {
             "id" : "upload_fastqcheck_to_qc_database",
             "label" : "upload_fastqcheck_to_qc_database"

diff --git a/lib/npg_pipeline/pluggable/registry.pm b/lib/npg_pipeline/pluggable/registry.pm
@@ -45,6 +45,7 @@ Readonly::Hash my %REGISTRY => (
   'upload_illumina_analysis_to_qc_database' => {'illumina_qc_archiver' => 'create'},
   'upload_fastqcheck_to_qc_database'        => {'fastqcheck_archiver' => 'create'},
   'upload_auto_qc_to_qc_database'           => {'autoqc_archiver' => 'create'},
+  'archive_run_data_to_irods'               => {'run_data_to_irods_archiver' => 'create'},
 
   'bam_cluster_counter_check'=> {'cluster_count' => 'create'},
   'seqchksum_comparator'     => {'seqchksum_comparator' => 'create'},