Jose Espinosa-Carrasco

> We are already removing duplicates with Picard MarkDuplicates right? Yes, the only thing is that chromap is not a peak caller but an aligner specially meant for aligning ChIP-seq,...

The command that the pipeline uses for aligning reads with `chromap` is: `chromap -l 2000 --SAM -t 2 -x genome.index -r genome.fa -1 SPT5_INPUT_REP2_T1_1_val_1.fq.gz -2 SPT5_INPUT_REP2_T1_2_val_2.fq.gz -o SPT5_INPUT_REP2_T1.Lb.sam`

After discussion in Slack with @lextallan seems [here](https://nfcore.slack.com/archives/CFP55NZ5G/p1659028321362489?thread_ts=1659026640.177489&cid=CFP55NZ5G) seems that the problem is the TLEN column in the files produced by `chromap` is empty: "Main issue for running chromap aligned...

This has been partially fixed in #290 by filtering out paired-end data when Chromap is used. However, once a new version of Chromap is released that output usable bam files,...

I tried with the same files of the current test dataset: ``` SRR1822153 SRR1822154 SRR1822157 SRR1822158 SRR5204809 SRR5204810 ``` And the same approach you used for the rnaseq pipeline (filtering...

I answered your query in slack, think that you are including an empty line at the end of the file. Let me know if this does not solve the problem.

I would say that the problem might be related to #128, maybe in some files no peaks are called. You could skip this process by adding the `--skip_consensus_peaks` parameter to...

This one could be also relevant for the implementation of the IDR analysis specifically for ChIP-seq analysis, implemented in NF: https://github.com/bioinfo-pf-curie/chip-seq

Yes, that could be an option, another one could be to have a separate file with the information about replicates... In the case we want to keep the samplesheet standard...

Yes, I agree two metadata files means increasing at least 2x the possibility of making mistakes :stuck_out_tongue_closed_eyes: