Hello, I'm working with the

nf-core/chipseq

pipeline and have met a challenge with my input controls. My ChIP-seq sample is single-end, and I have multiple input control samples: Single-end inputs:

SRR5339124.fastq.gz

,

SRR5339122.fastq.gz

,

SRR5339123.fastq.gz

Paired-end input:

SRR5339121_1.fastq.gz

and

SRR5339121_2.fastq.gz

When I include both single-end and paired-end input samples under the same

sample

and

replicate

identifiers in the

samplesheet.csv

, the pipeline throws an error:

ERROR: Please check samplesheet -> Multiple replicates of a sample must be of the same datatype i.e. single-end or paired-end!
Sample: 'Input'

I understand that the pipeline requires all sample replicates to be the same data type. To resolve this, I considered excluding the paired-end input to maintain consistency with the single-end ChIP sample. However, I'm concerned about the implications of these approaches on the analysis, especially regarding the accurate representation of input controls. So I wonder: - What is the recommended approach for handling such mixed input controls in nf-core/chipseq? - Is it acceptable to exclude the paired-end input, or is there a way to incorporate it without violating the pipeline's requirements? - Are there any best practices/suggestions for managing this scenario? Thanks a lot for the help!