Hi, I am running the latest chipseq pipeline (V 2.1.0), and the pipeline gets completed successfully. However, the MACS3 and DeSeq2 do not run (Attached screenshot). My arguments for running it is

nextflow run nf-core/chipseq --input ./input.csv --outdir ./results --genome GRCh38 -profile singularity --read_length 100 --max_cpus 5

Can someone tell me what went wrong? and what I should do to include MACS3 and DESEQ2 to run?

Hi! What does your sample sheet (input.csv) look like?

This is my file format of my input.csv

sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
H3K4me1_1,H3K4me1_1.fastq.gz,,1,,,
CTCF_1,CTCF_1.fastq.gz,,1,,,
CTCF_2,CTCF_2.fastq.gz,,1,,,
H3K4me1_2,H3K4me1_2.fastq.gz,,1,,,
CTCF_3,CTCF_3.fastq.gz,,1,,,
H3K27ac_1,H3K27ac_1.fastq.gz,,1,,,
H3K27ac_2,H3K27ac_2.fastq.gz,,1,,,
H3K27ac_3,H3K27ac_3.fastq.gz,,1,,,
H3K4me1_3,H3K4me1_3.fastq.gz,,1,,,
...

I just had the same issue. I'm also using single end data -- sample sheet looks identical except that I do have a control/control_replicate. I'm on

revision: 76e2382b6d [master]

. did you resolve this? If so, how?