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qc_conditions.yml
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qc_conditions.yml
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quast:
'# contigs (>= 1000 bp)':
warning:
condition_type: gt
condition_value: 75
failure:
condition_type: gt
condition_value: 150
'N50':
warning:
condition_type: lt
condition_value: 100000
failure:
condition_type: lt
condition_value: 50000
'Total length (>= 1000 bp)':
warning:
condition_type: lt_or_gt
condition_value:
- MIN_GENOME_LENGTH
- MAX_GENOME_LENGTH
fastqc:
'Basic Statistics':
warning:
condition_type: eq
condition_value: WARN
failure:
condition_type: eq
condition_value: FAIL
'Per base sequence quality':
failure:
condition_type: eq
condition_value: FAIL
'Per sequence quality scores':
failure:
condition_type: eq
condition_value: FAIL
'Per base sequence content':
warning:
condition_type: eq
condition_value: FAIL
'Per sequence GC content':
warning:
condition_type: eq
condition_value: FAIL
'Per base N content':
warning:
condition_type: eq
condition_value: FAIL
'Sequence Length Distribution':
failure:
condition_type: eq
condition_value: FAIL
'Sequence Duplication Levels':
warning:
condition_type: eq
condition_value: FAIL
'Overrepresented sequences':
failure:
condition_type: eq
condition_value: FAIL
'Adapter Content':
failure:
condition_type: eq
condition_value: FAIL
confindr:
'contam_status':
failure:
condition_type: eq
condition_value: 'True'
'percentage_contamination':
failure:
condition_type: gt
condition_value: 5
warning:
condition_type: gt
condition_value: 0
bactinspector:
'result':
warning:
condition_type: eq
condition_value: 'uncertain'
'species':
warning:
condition_type: eq
condition_value: ''
file_size_check:
'size':
failure:
condition_type: lt
condition_value: MIN_FILE_SIZE