Avoid error on unknown headers in input.csv about scrnaseq HOT 4 CLOSED

Hi,

this issue should be fixed in the development version.
You can give it a try with nextflow run ... -r dev. If it doesn't work, please let me know!

from scrnaseq.

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 fastq_1, but there is not a fastq_2.

The input.csv file is similar to:

"sample","fastq_1","fastq_2","strandedness",...
"id1","/path/to/fastq/sample1.fastq.gz","","auto",...

Please note how the fastq_2 column contains empty values.

I'm getting an error validating the 'input' again:

ERROR ~ ERROR: Validation of 'input' file failed!

 -- Check '.nextflow.log' file for details
The following errors have been detected:

* -- Entry 1: Missing required value: fastq_2
* -- Entry 2: Missing required value: fastq_2

Having an empty fastq_2 seems correct to me when I check the code at the master branch. There, if the fastq_2 is empty then the single_end variable is set to "1". You can see this below (specifically line 184, in the not fastq_2):

However on the dev branch, the input schema used for the fastq_2 validation must exist and can't be empty:

I'd like for the scrnaseq pipeline to accept an input file with a fastq_2 column filled with "" (empty strings), since that's what is generated by the nf-core/fetchngs pipeline when downloading datasets.

Thanks and sorry for the delay in the reply

from scrnaseq.

Just for further ideas, it may be good to checkout the rnaseq pipeline:

https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/assets/schema_input.json#L16-L46

from scrnaseq.

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?

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