Hi All, is there a very recent changes for the input samples.csv like within a month? I tried to run this samples.csv but got an error:

sample,fastq_1,fastq_2,antibody,control
AD1_Input_1,AD1_Input_1_S7_L002_R1_001.fastq.gz,AD1_Input_1_S7_L002_R2_001.fastq.gz,,
AD1_Input_2,AD1_Input_2_S8_L002_R1_001.fastq.gz,AD1_Input_2_S8_L002_R2_001.fastq.gz,,
AD1_FLAG_1,AD1_FLAG_1_S17_L002_R1_001.fastq.gz,AD1_FLAG_1_S17_L002_R2_001.fastq.gz,AD1_FLAG,AD1_Input
AD1_FLAG_2,AD1_FLAG_2_S18_L002_R1_001.fastq.gz,AD1_FLAG_2_S18_L002_R2_001.fastq.gz,AD1_FLAG,AD1_Input

and the error:

ERROR: Please check samplesheet -> Control identifier has to match does a provided sample identifier!
  Control: 'AD1_Input'

But I thought this matches the samplesheet on the https://nf-co.re/chipseq/2.0.0/docs/usage/ If remove the _1 and 2 from the AD1__Input samples, it works. So, does that mean the samplesheet input format has changed?

Not a recent change, just something that's been wrong in the documentation all along, see e.g. this issue from October 2022 (shortly after 2.0.0 was released): https://github.com/nf-core/chipseq/issues/320 However, if you switch to 2.1.0, the format is different: there is an explicit column for replicate number for the sample and the input/control.

@Anne Wenzel Thanks for your reply! That's helpful!