Nicolás A. Schcolnicov

Hi @FriederikeHanssen! I have been looking into this issue, since I was struggling with it too. In my case **I couldn't reproduce it using the Biocontainer "quay.io/biocontainers/control-freec:11.6--h1b792b2_1" image**. This image...

@FriederikeHanssen Thank you! Running it with the new container fixed the issue for me

Hi! I Just got this same error, it doesn't appear to be related to the new container update, since I was able to reproduce with both the old and new...

Hi @bounlu @FriederikeHanssen I kept researching this issue, and found this: When running the somatic tumor pair test dataset provided by sarek using this command line: ```nextflow run ../../main.nf -profile...

@bounlu @Teezi This PR fixed the issue for me, could you please check if you are still getting the error? Else we can close this issue

Hi @drkoryjohns this happened to me too, there is a parameter for chr_dir that you need to add, which should contain a list of fasta files, one for each chromosome...

Created a separate PR for this, because I couldn't push changes into @Aratz branch. https://github.com/nf-core/demultiplex/pull/220

Hi @OliverH96, this one is a bit tough to debug without being able to run the pipeline with the exact setting that you used. Would it be possible for you...

I recently tried to debug this, I used this command: nextflow run nf-core/smrnaseq -r dev -latest -profile docker --input https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet-full.csv --outdir results --with_umi false --mirtrace_species oar --fasta ../files/Ovis_aries_rambouillet.ARS-UI_Ramb_v2.0.dna.toplevel.fa.gz --mirna_gtf ../files/rumimir_sheep.gff...