Alex M. Ascensión

BTW, just in case, genome gtf and fasta files are downloaded according to nf-core/rnaseq guidelines, and STAR/salmon/kalisto indexes are built as in the code from the respective .nf files.

Hi! I realised that the problem might be related to the nomenclature of the transcript fasta and the gtf file. To build kallisto and salmon indexes I used the fasta...

Hi @JuliaSprenger, I'm using the SpikeInterface module to do the loading, so I'm not sure if I'd be able to do the PR. I was redirected by @alejoe91 to open...

I can't find it. They currently work with MATLAB files to load the data. I will try to contact them to see if they have some Python code for that...

Same!

Perfect! I tried the 1.0.2 version also and the error didn't appear.

Hi! My list of files is this: ``` database/indexes/GRCm38/aa_data_repo/mm10: annotations file_list.txt mm10-blacklist.v2.bed mm10_conserved_gain5.bed mm10.fa.amb mm10.fa.fai mm10.Hardison.Excludable.full.bed mm10_noAlt.fa.fai cancer file_sources.txt mm10_centromere.bed mm10_conserved_gain5_onco_subtract.bed mm10.fa.ann mm10.fa.pac mm10_k35.mappability.bedgraph onco_bed.bed dummy_ploidy.vcf last_updated.txt mm10_cnvkit_filtered_ref.cnn mm10.fa mm10.fa.bwt...

Hi! Now it seems to work, but I get the following error: ``` ERROR ~ Error executing process > 'NFCORE_CIRCDNA:CIRCDNA:AMPLICONSUITE (CDNA_3)' Caused by: Process `NFCORE_CIRCDNA:CIRCDNA:AMPLICONSUITE (CDNA_3)` terminated with an error...

Hi! Yes! It works fine. Thanks!

Hi! I've run the pipeline a second time with this config ``` nextflow run nf-core/circdna \ -r dev \ -profile docker \ -resume \ --max_cpus 9 \ --max_memory 53.GB \...