A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I've been running the `chipseq` pipeline for the first time with runs of the same sample over multiple lanes. I have come across this error from `picard MarkDuplicates` that I was hoping someone had an idea how to overcome?

``` Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once.  1: RGLH00392:127:22FL5GLT4:2:2446:16278:4138```

Hi, probably you have found already, but seems that adding the read group could help: <https://gatk.broadinstitute.org/hc/en-us/community/posts/4408717387803-SAMException-Value-was-put-into-PairInfoMap-more-than-once>

It seems that filtering our secondary alignments would be a work a round. Do you have any advice how to implement this? <https://www.biostars.org/p/176814/>

I have come across this too: <https://github.com/nf-core/eager/issues/655>

So I tried to botch together a `custom.config` with the following to ask bowtie2 to add read groups. But I'm a little naive as to how to get the pipeline to use the right `<Sample_Name>`, `<Sample_Name_Library>` etc.

```process {
        withName: 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN' {
                ext.args         = "--rg-id <Sample_Name> --rg SM:<Sample_Name> --rg LB:<Library_ID> --rg PU:<Sample_Name_Library_ID> --rg PL:<ILLUMINA>"
        }
}```
Could you please advise?

Looks like read groups are already added in the `conf/modules.config` <https://github.com/nf-core/chipseq/blob/76e2382b6d443db4dc2396e6831d1243256d80b0/conf/modules.config#L225-L252>