deseq2 missing

[mictadlo]

Description of the bug

Hi,
I ran the pipeline successfully, but in results folder I can not see any deseq2 output:

results> ls -1
fastp
fastqc
genome
multiqc
pipeline_info
star_salmon

What did I miss?

Command used and terminal output

> cat nfcorRNAseq_pbs.sh
#!/bin/bash -l
#PBS -N nfRNA
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
#PBS -m abe
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'

nextflow run nf-core/rnaseq \
      -profile singularity \
      -r 3.14.0 \
      --input samplesheet.csv \
      --fasta /work/waterhouse_team/NB/LAB360/NbLab360.genome.fasta \
      --save_reference \
      --gff /work/waterhouse_team/NB/LAB360/NbLab360.v103.gff.gz \
      --outdir results \
      --aligner star_salmon \
      --trimmer fastp \
      --extra_fastp_args detect_adapter_for_pe,correction \
      -resume

### Relevant files

cat samplesheet.csv
sample,fastq_1,fastq_2,strandedness
Lflower,data/Lflower_R1.fastq.gz,data/Lflower_R2.fastq.gz,auto
Lleaf,data/Lleaf_R1.fastq.gz,data/Lleaf_R2.fastq.gz,auto
Lroot,data/Lroot_R1.fastq.gz,data/Lroot_R2.fastq.gz,auto
Lseedl,data/Lseedl_R1.fastq.gz,data/Lseedl_R2.fastq.gz,auto
Lstem,data/Lstem_R1.fastq.gz,data/Lstem_R2.fastq.gz,auto

### System information

Singularity, HPC, PBSpro, SUSE Linux Enterprise Server 12 SP5, nf-core/rnaseq 3.14.0 

[pinin4fjords]

DESeq2 QC outputs should be present at star_salmon/deseq2_qc. Note that this pipeline doesn't do any differential analysis with DESeq2, see nf-core/differentialabundance if you'd like a pre-made solution for doing this.

Closing for now, but reopen if needed.