Hi, I have used the new updated rnssplice version and it has not been generating dexseq_dtu folder. Below is my code. It doesnt generate the output files for dexseq_dtu. Any reason. Attached is the execution text file

./nextflow run nf-core/rnasplice -r 1.0.4 \
   --input <> \
   --contrasts <> \
   --source fastq \
   --skip_fastqc \
   --fasta <>Mus_musculus.GRCm38.dna.primary_assembly.fa \
   --outdir <> \
   --aligner star_salmon \
   --dexseq_dtu \
   --dtu_txi dtuScaledTPM \
   --gtf <>Mus_musculus.GRCm38.100.gtf \
   --gtf_extra_attributes gene_id \
   --min_samps_gene_expr 0 \
   --min_samps_feature_expr 0 \
   --min_samps_feature_prop 0 \
   --min_feature_expr 0 \
   --min_feature_prop 0 \
   --min_gene_expr 0 \
   --edger_exon \
   --save_edger_plot \
   --igenomes_ignore \
   -profile singularity

I don't use this very often, but when I did there was a

star_salmon/dexseq_dtu

directory with the appropriate content. Interestingly, I did not even specify

--dexseq_dtu

(only `--dexseq_exon`; this was with version 1.0.3; I wonder if that parameter actually disables DTU by accident, instead of enabling it ...). Go through the

.nextflow.log

and see if there are any errors or warnings related to DEXSeq. While you are there, see which instances (if any) of the

DEXSEQ_DTU

process were running, and in which work directories. Then check these directories -- are the expected output files there, just not exported? Or did something go wrong? In the latter case, check the

.command.*

files for any clues. 🤞

I used 1.02 before and never had this issue before. I checked the .nextflow log, if fact it didnt give the dexseq_dtu output without the --min_samps_gene_expr 0 \ --min_samps_feature_expr 0 \ --min_samps_feature_prop 0 \ --min_feature_expr 0 \ --min_feature_prop 0 \ --min_gene_expr 0 \ I checked the log file, but it didnt tell me if dtu is enabled or disabled.

Can you search the

.nextflow.log

for

DEXSEQ_DTU

? E.g. with

less .nextflow.log

, then type

/DEXSEQ_DTU

, or with

grep

? There should be lines like

submitted process NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_STAR_SALMON:DEXSEQ_DTU (1) > jobId: ...

, as well as

[Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 123456; id: 123; name: NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_STAR_SALMON:DEXSEQ_DTU (1); status: COMPLETED ...

. If these are not there, DEXSeq was never run with DTU.