Comments (3)
annacprice
commented on June 1, 2024
clockwork:alignToRef fails when the top species hit does not have a corresponding reference genome. This error is expected and recorded in the error log.
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annacprice
commented on June 1, 2024
Error is recorded correctly, but samples should not be passing to clockwork:alignToRef when the top species hit does not have a corresponding reference genome
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annacprice
commented on June 1, 2024
Closed by 12a9412
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Related Issues (20)
- changes needed for vcfpredict sub-workflow HOT 1
- Update identify_tophit_and_contaminants2.py to reflect the new NCBI taxonomy HOT 2
- Add missing report generation to preprocessing:summarise HOT 2
- Empty contaminated.fa and failed in preprocessing:mapToContamFa process HOT 8
- species hits from Afanc missing dot abbreviations HOT 2
- Resource request in nextflow.config not working
- Empty contaminants.fa in preprocessing:downloadContamGenomes HOT 2
- preprocessing:identifyBacterialContaminants is identifying human reads as a contaminant to remove HOT 2
- Samples not passing to clockwork HOT 2
- Samples not passing to gnomonicus HOT 2
- AttributeError: 'list' object attribute 'append' is read-only in bin/create_final_json.py HOT 1
- Scripting/reporting still referring to mykrobe when it should refer to afanc HOT 2
- Error in read counting in preprocessing:fastp HOT 2
- Bash variables not being substituted in json HOT 2
- Minos fails when trying to compare against an empty VCF file HOT 4
- Bowtie2 database
- Unable to analyze single FASTQ reads HOT 1
- Additions for v0.9.8 HOT 1
- Singularity permissions error HOT 1
- intracellulare when statement bug HOT 1
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