Specifying minimap2 parameters

[lilif99]

Ask away!

Hi, I'm trying to specify the minimap2 parameter '--junc_bed' with a bed file of splice annotations to ensure the correct splice sites are mapped around my gene of interest, which is something that has worked well outside of this workflow. My code looks like this: nextflow run /home/lmf1u23/.nextflow/assets/epi2me-labs/wf-transcriptomes -resume --disable_ping true -profile apptainer -c /home/lmf1u23/nextflowa100_transcript.config --fastq ./FASTQ/CRA62.fastq --sample CRA62 --transcriptome_source reference-guided --ref_genome ./GCA_000001405.15_GRCh38_no_alt_analysis_set.fa --ref_annotation ./gencode.v41.annotations.gtf --out_dir ./CRA62/splice/ -with-apptainer ./epi2me.3 --cdna_kit SQK-PCS111 --pychopper_opts '-Q 5' --minimap2_opts '--junc_bed /home/lmf1u23/spliceannotations.bed' --min_feature_expr 2

But I keep getting an error at the pipeline:reference_assembly:map_reads step: [ERROR] unknown option in "--junc_bed"

Am I using it incorrectly or is this parameter not applicable for the epi2me wf?

[sarahjeeeze]

Thanks for letting us know, that is interesting. Could you let me know which minimap2 version you have locally? It might be that we need to update it in the workflow? minimap2 --version

[lilif99]

Hi @sarahjeeeze , I'm using the latest version of minimap2 2.28

[sarahjeeeze]

Ah ok we are on 2.24 - we will look at updating it and let you know when this is ready.