Closed rafalstepien closed 1 month ago
samplesheet.csv subsamplesheet.csv
Since I cannot attach .yaml
files below you will find raw config:
pep_version: "2.0.0"
sample_table: "samplesheet.csv"
subsample_table: "subsamplesheet.csv"
sample_table_index: "sample"
subsample_table_index: "sample"
The direct cause of this error is that in peppy.Project
initialization attributes self.st_index
and self.sst_index
are created. Unfortunately in further part of the script hardcoded variables (SAMPLE_NAME_ATTR
and SUBSAMPLE_NAME_ATTR
) are used instead of newly created attributes.
probably a relic of the time before this was a variable option
After resolving the first issue, the command eido convert pep_files/config.yaml -f csv
finishes with success announcement, but there are warnings:
Could not set subsample_table index. At least one of the requested columns does not exist: sample
Could not set subsample_table index. At least one of the requested columns does not exist: sample
Output file also does not look correctly: converted.csv
after running this command:
eido convert /home/bnt4me/virginia/repos/peppy/tests/data/example_peps-master/example_nextflow_subsamples/project_config.yaml --f csv --st-index sample --sst-index sample >> new.csv
From my side eido produces correct csv file: new.csv
Closing this issue
For PEP project which defines
sample_table_index
other than default (sample_name
) the following error is raised:Because of that I can't use
eido convert
command sucessfully.