Comments (3)
yep this restructure is bad and needs to be tested properly
from porecov.
Summary report generation should be safe against column order changes, as data is read into a pandas dataframe and accessed via column names.
So if column names didnt change it should work
from porecov.
Summary report generation should be safe against column order changes, as data is read into a pandas dataframe and accessed via column names.
So if column names didnt change it should work
yep, just checked it. Only the JSON-extraction shell script relies on column numbers. I will do some tests and send a PR soon
from porecov.
Related Issues (20)
- add skip scorpio parameter to pangolin HOT 1
- Only calculate NanoPlot after read filtering step HOT 5
- Add new V5 ARTIC primer BED HOT 5
- Medaka step fails in the -profile fastq_test HOT 3
- summary_report.py fails HOT 7
- publish primersitereport from medaka output
- VarSkipV2b primer does not work as expected HOT 7
- Update Medaka to support R10.4.1 models HOT 14
- Update --help to list up-to-date primer schemes that are supported
- MinKNOW/Guppy update needs new model for R10.4.1 5 kHz HOT 6
- Warning when execution report and timeline already exists HOT 1
- The pipeline fails in artic_ncov_wf_artic_medaka HOT 7
- new pangolin table columns HOT 1
- CovarPlot fails w/ custom BED HOT 5
- Process retry in slurm profile HOT 1
- Publish VCF files HOT 2
- Update medaka to get the latest models HOT 1
- Test Freyja Update function HOT 11
- [Question] CI for Variant Calling HOT 5
- Singularity container execution of pangolin crashes with recent nextflow versions HOT 9
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from porecov.