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parameter must now be a list once again. (#142)
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* parameter must now be a list once again.

legacy qcjob configurations removed.

* bugfix
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@charles-cowart
charles-cowart authored Jun 14, 2024
1 parent b9bdc00 commit d7d5e7e
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Showing 7 changed files with 12 additions and 139 deletions.
25 changes: 2 additions & 23 deletions sequence_processing_pipeline/tests/data/configuration_profiles/iseq_metagenomic.json
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Expand Up @@ -25,33 +25,12 @@
"executable_path": "bcl-convert",
"per_process_memory_limit": "10gb"
},
"qc": {
"nodes": 1,
"nprocs": 16,
"queue": "qiita",
"wallclock_time_in_minutes": 60,
"minimap2_databases": [
"/databases/minimap2/human-phix-db.mmi"
],
"kraken2_database": "/databases/minimap2/hp_kraken-db.mmi",
"modules_to_load": [
"fastp_0.20.1",
"samtools_1.12",
"minimap2_2.18"
],
"fastp_executable_path": "fastp",
"minimap2_executable_path": "minimap2",
"samtools_executable_path": "samtools",
"job_total_memory_limit": "20gb",
"job_pool_size": 30,
"job_max_array_length": 1000
},
"nu-qc": {
"nodes": 1,
"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",
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}
}
}
}
}
25 changes: 2 additions & 23 deletions sequence_processing_pipeline/tests/data/configuration_profiles/miseq_amplicon.json
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Expand Up @@ -25,33 +25,12 @@
"executable_path": "bcl-convert",
"per_process_memory_limit": "10gb"
},
"qc": {
"nodes": 1,
"nprocs": 16,
"queue": "qiita",
"wallclock_time_in_minutes": 60,
"minimap2_databases": [
"/databases/minimap2/human-phix-db.mmi"
],
"kraken2_database": "/databases/minimap2/hp_kraken-db.mmi",
"modules_to_load": [
"fastp_0.20.1",
"samtools_1.12",
"minimap2_2.18"
],
"fastp_executable_path": "fastp",
"minimap2_executable_path": "minimap2",
"samtools_executable_path": "samtools",
"job_total_memory_limit": "20gb",
"job_pool_size": 30,
"job_max_array_length": 1000
},
"nu-qc": {
"nodes": 2,
"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",
Expand Down Expand Up @@ -92,4 +71,4 @@
}
}
}
}
}
25 changes: 2 additions & 23 deletions sequence_processing_pipeline/tests/data/configuration_profiles/miseq_metagenomic.json
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Expand Up @@ -25,33 +25,12 @@
"executable_path": "bcl-convert",
"per_process_memory_limit": "10gb"
},
"qc": {
"nodes": 1,
"nprocs": 16,
"queue": "qiita",
"wallclock_time_in_minutes": 60,
"minimap2_databases": [
"/databases/minimap2/human-phix-db.mmi"
],
"kraken2_database": "/databases/minimap2/hp_kraken-db.mmi",
"modules_to_load": [
"fastp_0.20.1",
"samtools_1.12",
"minimap2_2.18"
],
"fastp_executable_path": "fastp",
"minimap2_executable_path": "minimap2",
"samtools_executable_path": "samtools",
"job_total_memory_limit": "20gb",
"job_pool_size": 30,
"job_max_array_length": 1000
},
"nu-qc": {
"nodes": 2,
"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",
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}
}
}
}
}
25 changes: 2 additions & 23 deletions sequence_processing_pipeline/tests/data/configuration_profiles/novaseq_amplicon.json
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Expand Up @@ -25,33 +25,12 @@
"executable_path": "bcl-convert",
"per_process_memory_limit": "10gb"
},
"qc": {
"nodes": 1,
"nprocs": 16,
"queue": "qiita",
"wallclock_time_in_minutes": 60,
"minimap2_databases": [
"/databases/minimap2/human-phix-db.mmi"
],
"kraken2_database": "/databases/minimap2/hp_kraken-db.mmi",
"modules_to_load": [
"fastp_0.20.1",
"samtools_1.12",
"minimap2_2.18"
],
"fastp_executable_path": "fastp",
"minimap2_executable_path": "minimap2",
"samtools_executable_path": "samtools",
"job_total_memory_limit": "20gb",
"job_pool_size": 30,
"job_max_array_length": 1000
},
"nu-qc": {
"nodes": 4,
"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",
Expand Down Expand Up @@ -92,4 +71,4 @@
}
}
}
}
}
25 changes: 2 additions & 23 deletions sequence_processing_pipeline/tests/data/configuration_profiles/novaseq_metagenomic.json
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Expand Up @@ -25,33 +25,12 @@
"executable_path": "bcl-convert",
"per_process_memory_limit": "10gb"
},
"qc": {
"nodes": 1,
"nprocs": 16,
"queue": "qiita",
"wallclock_time_in_minutes": 60,
"minimap2_databases": [
"/databases/minimap2/human-phix-db.mmi"
],
"kraken2_database": "/databases/minimap2/hp_kraken-db.mmi",
"modules_to_load": [
"fastp_0.20.1",
"samtools_1.12",
"minimap2_2.18"
],
"fastp_executable_path": "fastp",
"minimap2_executable_path": "minimap2",
"samtools_executable_path": "samtools",
"job_total_memory_limit": "20gb",
"job_pool_size": 30,
"job_max_array_length": 1000
},
"nu-qc": {
"nodes": 4,
"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",
Expand Down Expand Up @@ -92,4 +71,4 @@
}
}
}
}
}
25 changes: 2 additions & 23 deletions ...nce_processing_pipeline/tests/data/configuration_profiles/novaseq_metatranscriptomic.json
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Expand Up @@ -25,33 +25,12 @@
"executable_path": "bcl-convert",
"per_process_memory_limit": "10gb"
},
"qc": {
"nodes": 1,
"nprocs": 16,
"queue": "qiita",
"wallclock_time_in_minutes": 60,
"minimap2_databases": [
"/databases/minimap2/human-phix-db.mmi"
],
"kraken2_database": "/databases/minimap2/hp_kraken-db.mmi",
"modules_to_load": [
"fastp_0.20.1",
"samtools_1.12",
"minimap2_2.18"
],
"fastp_executable_path": "fastp",
"minimap2_executable_path": "minimap2",
"samtools_executable_path": "samtools",
"job_total_memory_limit": "20gb",
"job_pool_size": 30,
"job_max_array_length": 1000
},
"nu-qc": {
"nodes": 1,
"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",
Expand Down Expand Up @@ -92,4 +71,4 @@
}
}
}
}
}
1 change: 0 additions & 1 deletion sequence_processing_pipeline/tests/test_Pipeline.py
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Expand Up @@ -1562,7 +1562,6 @@ def test_configuration_profiles(self):
# output and make sure they are set to the default values found in
# default.json.
self.assertEqual(obs['bcl-convert']['nprocs'], 16)
self.assertEqual(obs['qc']['wallclock_time_in_minutes'], 60)

# assert increased values over default found in novaseq 6000/
# metagenomic profile are found in the final configuration as well.
Expand Down

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