(message moved from #C043FMKUNLB) Hi nf-core community ! I am new in nf-core and particularly interested in chipseq pipeline. I have several experimental conditions (let's consider ctcf and h3k4me1) and for both conditions, the same "ChIP inputs" (no antibody). As explained in the documentation, I should have a samplesheet.csv file like this:

sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
INP_Adipose,/path/to/reads/Input/Input1_Adipose.fastq.gz,,1,,,
INP_Adipose,/path/to/reads/Input/Input2_Adipose.fastq.gz,,1,,,
CTCF_Adipose,/path/to/reads/CTCF/CTCF_Adipose_rep1.fastq.gz,,1,CTCF,INP_Adipose,1
H3K27ac_Adipose,/path/to/reads/H3K27ac/H3K27ac_Adipose_rep1.fastq.gz,,1,H3K27ac,INP_Adipose,1

Because it is my first time use of the pipeline (and nf-core), I would like to split my runs into 2: 1 run for ctcf analysis, the other one for h3k4me1. Then I would have something like

sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
INP_Adipose,/path/to/reads/Input/Input1_Adipose.fastq.gz,,1,,,
INP_Adipose,/path/to/reads/Input/Input2_Adipose.fastq.gz,,1,,,
CTCF_Adipose,/path/to/reads/CTCF/CTCF_Adipose_rep1.fastq.gz,,1,CTCF,INP_Adipose,1

for ctcf samplesheet.csv and something like

sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
INPUT LINE(S) ?
H3K27ac_Adipose,/path/to/reads/H3K27ac/H3K27ac_Adipose_rep1.fastq.gz,,1,H3K27ac,INP_Adipose,1

for h3k4me1 samplesheet.csv. The aims of splitting: 1. find quickly where the errors come from (if any) 2. manage data storage (which is unfortunately not infinite) to keep what is useful for me and release space for next run 3. do 4. not run input calculation for each sample and reuse what I called "ChIP 5. inputs" from previous run instead (as it would do if I use the full 6. samplesheet.csv) The image is to complete the message (red numbers are for reading order). Thank you all for your responses, have a nice day 🙂

Any idea @Jose Espinosa-Carrasco by any chance?

Not sure I understand what the question is 🤔

From what I understand @Noémien wants to use some output from a previous run of chipseq in a second run of chipseq

OK thanks for the clarification, I am afraid you are not able to use the resulting bam files from a previous run you can only re-use all the reference, indexes generated in a first run, one thing you can do is start with a couple of samples for testing and then add the rest of the samples and

-resume

the pipeline, but this won’t fix the problem with the storage if it is limited

Ok thank you for your answer and for Maxime's clarification, that was the point. I will find the best way to manage my data 🙂