--protocol sequence not passed to mirtrace?

[JanineRoy]

Description of the bug

We have data created using QIASEQ protocol.
When setting --protocol "qiaseq" and investigating mirtrace QC output, no adapter got removed.
Output from mirtrace:

but mirtop creates a file with many mirna counts.

Nevertheless, when directly stating --three_prime_clip_r1 0 --clip_r1 0 --three_prime_adapter "AACTGTAGGCACCATCAAT" (please not that this is the same sequence as in the --protocol "qiaseq"), mirtrace is able to remove adapter:

but then the downstream analysis breaks (mirtop, MULTIQC).
The above also only works, when I do not state --protocol "custom", otherwise mirtrace breaks. Seems like there is no "custom" defined in mirtrace.

maybe related to?
#168

Command used and terminal output

# this lets mirtrace remove adapter, but mirtope and multiQC fail
nextflow run nf-core/smrnaseq -profile bi,cluster --input smRNASeq_input_test.csv \
--outdir 00_test_smRNAseq_qiaseq_as_custom/ --genome GRCh38 -r dev --mirtrace_species "hsa"  \
--skip_mirdeep \
--three_prime_clip_r1 0 --clip_r1 0 --three_prime_adapter "AACTGTAGGCACCATCAAT"

# this lets mirtop create a good looking result, but mirtrace is not able to remove adapters
nextflow run nf-core/smrnaseq -profile bi,cluster --input smRNASeq_input_test.csv \
--outdir 00_test_smRNAseq_qiaseq/ \
--genome GRCh38 -r dev --mirtrace_species "hsa" --protocol "qiaseq" --skip_mirdeep

Relevant files

No response

System information

Nextflow version 22.04.0

[apeltzer]

Fixed in dev