FastQ files from UMI-tools not being passed to fastp

[ilwookkim]

Description of the bug

Hi guys,

I tried to use Fastp instead of trimglore with umi deduplciation workflow as below, and it works fine with bash script.

1. umi tools : extract
2. fastp
3. star : align
4. umi tools : dedup
5. samtools : sort
6. rsem

When I choose trimglore (defalut) in nfcore/rnaseq, umi tools could extract umi and could deduplicate later.
But with Fastp, all umi tags are missing on the header of bam files, therefore it could not deduplicate.
Could you fix the bug?

the examples of params files content are below:

NOT WORK:

{
"outdir": "/home/",
"with_umi": true,
"umitools_extract_method": "regex",
"umitools_bc_pattern2": "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*",
"trimmer": "fastp"
}

WORK:

{
"outdir": "/home/",
"with_umi": true,
"umitools_extract_method": "regex",
"umitools_bc_pattern2": "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*",
}

Thanks,
Best.

Kim

Command used and terminal output

nextflow run nf-core/rnaseq -r 3.11.1 -with-report ./nf_core.html -params-file ./nf_params.json --input ./samplesheet.csv -profile singularity -resume

Relevant files

No response

System information

No response