address review comments

EBIvariation · May 10, 2024 · 14557c8 · 14557c8
1 parent d556d08
commit 14557c8
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diff --git a/eva-accession-release-automation/README.md b/eva-accession-release-automation/README.md
@@ -9,7 +9,6 @@ pip install -e /path/to/eva-accession/eva-accession-release-automation
 The release automation script `run_release_for_species.py` has the following parameters:
 * **common-release-properties-file:** Path to yaml config file, see below
 * **taxonomy-id:** Taxonomy to release
-* **memory:** Amount of memory to use when running the release jobs
 
 You also need to set `PYTHONPATH=/path/to/eva-accession/eva-accession-release-automation/run_release_in_embassy`.
 

diff --git a/eva-accession-release-automation/run_release_in_embassy/run_release_for_assembly.nf b/eva-accession-release-automation/run_release_in_embassy/run_release_for_assembly.nf
@@ -14,9 +14,11 @@ process initiate_release_status_for_assembly {
     label 'short_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -29,9 +31,11 @@ process copy_accessioning_collections_to_embassy {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -44,9 +48,11 @@ process run_release_for_assembly {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -59,9 +65,11 @@ process merge_dbsnp_eva_release_files {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -74,9 +82,11 @@ process sort_bgzip_index_release_files {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -89,9 +99,11 @@ process validate_release_vcf_files {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -104,9 +116,11 @@ process analyze_vcf_validation_results {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -119,9 +133,11 @@ process count_rs_ids_in_release_files {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -134,9 +150,11 @@ process validate_rs_release_files {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -149,9 +167,11 @@ process update_sequence_names_to_ena {
     label 'long_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag
+    val true, emit: flag
+
     script:
     """
     export PYTHONPATH=$params.python_path
@@ -164,9 +184,11 @@ process update_release_status_for_assembly {
     label 'short_time', 'med_mem'
 
     input:
-        val flag
+    val flag
+
     output:
-        val true, emit: flag11
+    val true, emit: flag11
+
     script:
     """
     export PYTHONPATH=$params.python_path

diff --git a/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py b/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py
@@ -40,7 +40,6 @@ def get_nextflow_params(taxonomy_id, assembly_accession, release_version):
         'jar': cfg['jar'],
         'log_file': get_release_log_file_name(taxonomy_id, assembly_accession),
         'maven': cfg['maven'],
-        'python_script': cfg.query('python', 'interpreter'),
         'python_path': os.environ['PYTHONPATH'],
         'release_version': release_version,
         'assembly_folder': release_dir,
@@ -121,16 +120,10 @@ def main():
     argparse.add_argument("--release_version", required=True)
     argparse.add_argument("--resume", default=False, required=False,
                           help="Resume the nextflow pipeline for the specified taxonomy and assembly")
-    argparse.add_argument("--release_config_file",
-                          help="Path to the release configuration file. That will override the config specified with "
-                               "RELEASE_CONFIG variable or placed in ~/.release_config.yml.",
-                          required=False)
     args = argparse.parse_args()
-
+    load_config()
     logging_config.add_stdout_handler()
 
-    load_config(args.release_config_file)
-
     run_release_for_species(args.taxonomy_id, args.assembly_accessions, args.release_version, args.resume)