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

nf-core

Anyone else having issues with the PG field / line in the bam header when using fq2bam ?

if you want to run mutect afterwards you have to set the command line flags correctly for example

```            // Using specific read group tags for mutect compability (keep if using mutect)
            "--read-group-id-prefix ${meta.sample_lane_id}",
            "--read-group-sm ${meta.patient}_${meta.sample}",
            "--read-group-lb ${meta.sample}",
            "--read-group-pl ${params.seq_platform}",```

Basically the bam files have this line on the header:

```@PG	ID:pbrun fq2bam	PN:pbrun fq2bam	VN:4.6.0-1	CL:pbrun fq2bam --ref ./NA12878.fa --in-fq 236195_R1.trim.fastq.gz 236195_R2.trim.fastq.gz --out-bam 236195.bam --num-gpus 1 --bwa-cpu-thread-pool 32 --monitor-usage --tmp-dir /tmp/nxf.8aeGGnQ1V3```

And the fact that thre is a space between 'pbrun fq2bam' crashes on some downstream tools for me.

I am already passing a RG line like this (in nextflow):

"--in-fq ${reads[0]} ${reads[1]} \"@RG\\tID:A\\tPU:A\\tLB:LIB1\\tPL:ILLUMINA\\tSM:SAMPLE1\""

But I don't see a way to change the PG line? I guess I can reheader but it's unideal for my pipeline.

For me passing the RG line did not work i could only handle sthis via the spoecific fq2bam flags so I guess you should be able to do that when you set it like I did (then there will be no more space added in your id I suppose)

It took some trial and error for me until I figured out how to control the header properly

But the line that breaks for me is not RG but PG, which I can;t set within fq2bam afaik?

Let me grab my notes and find this because I tried out many things maybe I touched the PG line at some point

I think judging from the man page:
<https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam.html>
I would still try to modify this `--read-group-id-prefix ${meta.sample_lane_id}` and hope that the changes reflect to the header (so that it does not set the generic tool name "pbrun fq2bam")?

But are you really sure that the header breaks your downstream tools? What tools are those? Because the header is only metadata?

I am afraid I do not find anything - i guess my issue were infact only these ID fields and never the header :confused:

In any case I guess that is an oversight by nvidia because it would be better to return `pbrun-fq2bam` so `-` instead of a space. <@U05LY7TP5SL> maybe you can forward that to your dev team :slightly_smiling_face:

Thank you for tagging me. Let me catch up on this to understand what the issue is. I am happy to submit a bug / feature request to the engineering team.

<@U05M4JGNWKG> What downstream tools are you using?

They are mainly custom tools but I'm looking into whether that's actually causing the issue since as Famke said that should only be metadata. Let me get back to you soon.