add release step to copy to ftp

move pipelines to new folder

Author: emmaco

cwl/test/workflows/workflow_tests.yml

@@ -4,7 +4,7 @@
 # Genome scanner
 - doc: Functional tests for genome scanner
   job: genome_scanner/test.yml
-  tool: ../../workflows/genome_scanner.cwl
+  tool: ../../release/genome_scanner.cwl
   should_fail: false
   output:
     cmsearch_matches:

cwl/wrapper_scripts/process_dir.py

@@ -33,7 +33,7 @@
 
 current_dir = os.path.dirname(__file__)
 
-WORKFLOW_PATH = os.path.realpath(os.path.join(current_dir, os.pardir, 'workflows', 'nc_rna_workflow.cwl'))
+WORKFLOW_PATH = os.path.realpath(os.path.join(current_dir, os.pardir, 'release', 'nc_rna_workflow.cwl'))
 
 REFERENCE_CM_DB = os.path.realpath(os.path.join(current_dir, os.pardir, 'db', REFERENCE_DB_NAME))
 

pdb_mapping/nextflow.config pipelines/pdb/nextflow.config

@@ -0,0 +1,33 @@
+nextflow.enable.dsl=2
+
+process generate_seed_files {
+    memory '10GB'
+
+    output:
+    val('done)')
+
+    """
+    rm -rf ${params.release_ftp}/seed/
+    mkdir -p ${params.release_ftp}/seed/
+    python ${params.rfamprod}/scripts/export/generate_ftp_files.py --acc all --seed --dest-dir "${params.release_ftp}/seed"
+    """
+
+}
+
+workflow copy_to_release_ftp {
+    emit:
+        done
+    main:
+        copy_seed_files \
+        copy_cm_files \
+        copy_genome_browser \
+        copy_fasta \
+        copy_tree \
+        copy_files \
+
+        | set { done }
+}
+
+workflow {
+    copy_to_release_ftp()
+}

pdb_mapping/pdb_mapping.nf pipelines/pdb/pdb_mapping.nf

@@ -3,14 +3,16 @@
 nextflow.enable.dsl = 2
 
 include { generate_annotated_files } from './annotated_files'
-include { mapping_and_updates } from 'pdb_mapping/pdb_mapping'
+include { mapping_and_updates } from 'pdb/pdb_mapping'
 include { view_process } from './view_process'
 include { clan_competition } from './clan_competition'
 include { prepare_rfam_live } from './prepare_rfam_live'
 include { generate_ftp_files } from './generate_ftp_files'
 include { generate_rfam2go } from './rfam2go'
 include { stage_rfam_live } from './stage_rfam_live'
 include { text_search } from './update_text_search_dev'
+include { copy_to_release_ftp } from './copy_to_release_ftp'
+
 
 
 workflow {
@@ -30,5 +32,7 @@ workflow {
   | ifEmpty('no rfam2go') \
   | stage_rfam_live \
   | ifEmpty('no stage rfam_live') \
-  | text_search
+  | text_search \
+  | ifEmpty('no stage text_search') \
+  | copy_to_release_ftp
 }