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Avoid error on unknown headers in input.csv #302
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Hi, this issue should be fixed in the development version. |
Hi @grst I have been able now to test the dev pipeline. Thanks for the update. Unfortunately I am still facing validation issues: I am using a single end dataset, where there is a The input.csv file is similar to:
Please note how the I'm getting an error validating the 'input' again:
Having an empty scrnaseq/bin/check_samplesheet.py Lines 181 to 187 in 90cb6a4
However on the scrnaseq/assets/schema_input.json Lines 16 to 30 in 1043441
I'd like for the scrnaseq pipeline to accept an input file with a Thanks and sorry for the delay in the reply |
Just for further ideas, it may be good to checkout the rnaseq pipeline: |
The check is done on purpose. All protocols supported by this pipeline use paired end data, where R1 contains UMI/barcode and R2 the actual sequence. What kind of single-cell data are you dealing with? |
Description of feature
The
nf-co.re/rnaseq
pipeline accepts and ignores any extra column ininput.csv
that is not required by the pipeline. This is useful because I can reuse theinput.csv
or include additional information I want to use in downstream analyses, without having to generate a specificinput.csv
just for running the pipeline.This
scrnaseq
pipeline is much more strict, giving an error when any unknown column is found.I would rather for the
scrnaseq
pipeline to follow thernaseq
behaviour, following the robustness principle that one should "be conservative in what you send, be liberal in what you accept".Is there any specific reason why you are not as liberal accepting unknown columns in the
input.csv
file?Thanks!
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