Updates to support movi filtering updates in mg-scripts. (#87)

Author: charles-cowart

qp_klp/Step.py

@@ -330,7 +330,10 @@ def _quality_control(self, config, input_file_path):
                            config['known_adapters_path'],
                            bucket_size=config['bucket_size'],
                            length_limit=config['length_limit'],
-                           cores_per_task=config['cores_per_task'])
+                           cores_per_task=config['cores_per_task'],
+                           movi_path=config['movi_executable_path'],
+                           gres_value=config['gres_value'],
+                           pmls_path=config['pmls_path'])
 
         nuqc_job.run(callback=self.update_callback)
 

qp_klp/tests/data/configuration_profiles/iseq_metagenomic.json

@@ -51,7 +51,7 @@
         "cpus_per_task": 8,
         "queue": "qiita",
         "wallclock_time_in_minutes": 240,
-        "minimap2_databases": "/scratch/databases/minimap2",
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -65,7 +65,10 @@
         "known_adapters_path": "fastp_known_adapters_formatted.fna",
         "bucket_size": 8,
         "length_limit": 100,
-        "cores_per_task": 4
+        "cores_per_task": 4,
+        "movi_executable_path": "/home/user/user_dir/Movi/build/movi-default",
+        "gres_value": 4,
+        "pmls_path": "/home/user/user_dir/human_host_filtration/scripts/qiita_filter_pmls.py"
       },
       "seqpro": {
         "seqpro_path": "seqpro",

qp_klp/tests/data/configuration_profiles/miseq_amplicon.json

@@ -19,7 +19,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2028,
-        "minimap2_databases": "/scratch/databases/minimap2",
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -33,7 +33,10 @@
         "known_adapters_path": "fastp_known_adapters_formatted.fna",
         "bucket_size": 8,
         "length_limit": 100,
-        "cores_per_task": 2
+        "cores_per_task": 2,
+        "movi_executable_path": "/home/user/user_dir/Movi/build/movi-default",
+        "gres_value": 4,
+        "pmls_path": "/home/user/user_dir/human_host_filtration/scripts/qiita_filter_pmls.py"
       },
       "seqpro": {
         "seqpro_path": "seqpro",

qp_klp/tests/data/configuration_profiles/miseq_metagenomic.json

@@ -30,7 +30,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2028,
-        "minimap2_databases": "/scratch/databases/minimap2",
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -44,7 +44,10 @@
         "known_adapters_path": "fastp_known_adapters_formatted.fna",
         "bucket_size": 8,
         "length_limit": 100,
-        "cores_per_task": 2
+        "cores_per_task": 2,
+        "movi_executable_path": "/home/user/user_dir/Movi/build/movi-default",
+        "gres_value": 2,
+        "pmls_path": "/home/user/user_dir/human_host_filtration/scripts/qiita_filter_pmls.py"
       },
       "seqpro": {
         "seqpro_path": "seqpro",

qp_klp/tests/data/configuration_profiles/miseq_metatranscriptomic.json

@@ -30,7 +30,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2028,
-        "minimap2_databases": "/scratch/databases/minimap2",
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -44,7 +44,10 @@
         "known_adapters_path": "fastp_known_adapters_formatted.fna",
         "bucket_size": 8,
         "length_limit": 100,
-        "cores_per_task": 2
+        "cores_per_task": 2,
+        "movi_executable_path": "/home/user/user_dir/Movi/build/movi-default",
+        "gres_value": 4,
+        "pmls_path": "/home/user/user_dir/human_host_filtration/scripts/qiita_filter_pmls.py"
       },
       "seqpro": {
         "seqpro_path": "seqpro",

qp_klp/tests/data/configuration_profiles/novaseq_amplicon.json

@@ -19,7 +19,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2048,
-        "minimap2_databases": "/scratch/databases/minimap2",
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -33,7 +33,10 @@
         "known_adapters_path": "fastp_known_adapters_formatted.fna",
         "bucket_size": 8,
         "length_limit": 100,
-        "cores_per_task": 4
+        "cores_per_task": 4,
+        "movi_executable_path": "/home/user/user_dir/Movi/build/movi-default",
+        "gres_value": 4,
+        "pmls_path": "/home/user/user_dir/human_host_filtration/scripts/qiita_filter_pmls.py"
       },
       "seqpro": {
         "seqpro_path": "seqpro",

qp_klp/tests/data/configuration_profiles/novaseq_metagenomic.json

@@ -30,7 +30,7 @@
         "cpus_per_task": 32,
         "queue": "qiita",
         "wallclock_time_in_minutes": 2048,
-        "minimap2_databases": "/scratch/databases/minimap2",
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -44,7 +44,10 @@
         "known_adapters_path": "fastp_known_adapters_formatted.fna",
         "bucket_size": 8,
         "length_limit": 100,
-        "cores_per_task": 4
+        "cores_per_task": 4,
+        "movi_executable_path": "/home/user/user_dir/Movi/build/movi-default",
+        "gres_value": 4,
+        "pmls_path": "/home/user/user_dir/human_host_filtration/scripts/qiita_filter_pmls.py"
       },
       "seqpro": {
         "seqpro_path": "seqpro",

qp_klp/tests/data/configuration_profiles/novaseq_metatranscriptomic.json

@@ -51,7 +51,7 @@
         "cpus_per_task": 8,
         "queue": "qiita",
         "wallclock_time_in_minutes": 240,
-        "minimap2_databases": "/scratch/databases/minimap2",
+        "minimap2_databases": ["/databases/minimap2/db_1.mmi", "/databases/minimap2/db_2.mmi"],
         "modules_to_load": [
           "fastp_0.20.1",
           "samtools_1.12",
@@ -65,7 +65,10 @@
         "known_adapters_path": "fastp_known_adapters_formatted.fna",
         "bucket_size": 8,
         "length_limit": 100,
-        "cores_per_task": 4
+        "cores_per_task": 4,
+        "movi_executable_path": "/home/user/user_dir/Movi/build/movi-default",
+        "gres_value": 4,
+        "pmls_path": "/home/user/user_dir/human_host_filtration/scripts/qiita_filter_pmls.py"
       },
       "seqpro": {
         "seqpro_path": "seqpro",