Hi! I'm trying to run rnaseq the first time, using fastp for trimming and then kallisto pseudoalignment, but get stuck on an error. I run as a slurm script containing these input parameters:

module purge
module load PDC apptainer
module load nextflow/25.04.7

nextflow run nf-core/rnaseq -r 3.26.0 \
    -resume \
    --input /cfs/klemming/projects/snic/uppstore2017202/CSPR/CSPR_nfcore/samplesheet_SUBSET.csv \
    --gtf /cfs/klemming/projects/snic/uppstore2017202/CSPR/CSPR_nfcore/references/Cricetulus_griseus_picr.CriGri-PICRH-1.0.115.ADDONS.gtf.gz \
    --transcript_fasta /cfs/klemming/projects/snic/uppstore2017202/CSPR/CSPR_nfcore/references/Cricetulus_griseus_picr.CriGri-PICRH-1.0.cdna.all.ADDONS.fa.gz \
    --outdir /cfs/klemming/projects/snic/uppstore2017202/CSPR/CSPR_nfcore/CSPR_KALLISTO_SUBSET \
    --save_reference true \
    --trimmer fastp \
    --extra_fastp_args="--trim_poly_g" \
    --skip_alignment true \
    --pseudo_aligner kallisto \
    -profile pdc_kth

the NBIS supporters suggested I post this as the relevant part of the .nextflow.log:

"Aug-18 10:10:39.662 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 23591666; id: 7; name: NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FAST QC_UMITOOLS_FASTP:FASTQC_RAW (P15053_155); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/uppstore2017202/CSPR/CSPR_nfcore/work/32/3a62dee4391d5da0ce1d5ba32f1c94 started: 17 87040184069; exited: 2026-08-18T08:10:34Z; ] Aug-18 10:13:14.672 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[jobId: 23591911; id: 10; name: NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (P15053_155); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/p rojects/supr/uppstore2017202/CSPR/CSPR_nfcore/work/75/f9ece9da17b459f7f5d252ce77a712 started: 1787040554642; exited: -; ] ~> TaskHandler[jobId: 23591912; id: 9; name: NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM (P15053_155); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/uppstore2017202/CSPR/CSPR_nfcore/work/25/4a70771faf8ae215578db8361afc4e started: 1787040554644; exited: -; ] Aug-18 10:14:04.781 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 23591911; id: 10; name: NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_A FTER_TRIMMING (P15053_155); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/uppstore2017202/CSPR/CSPR_nfcore/work/75/f9ece9da17b459f7f5d252ce77a712 started: 1787040554642; ex ited: 2026-08-18T08:14:01Z; ] Aug-18 10:14:05.056 [Actor Thread 46] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 2 FASTQ files Aug-18 10:14:05.228 [Actor Thread 41] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX; work-dir=null error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: java.util.LinkedHashMap ([id:P15053_155, strandedness:auto, seq_platform:[], seq_center:[], single_end:false, ha s_genome_bam:false, has_transcriptome_bam:false, original_genome_bam:null, original_transcriptome_bam:null]) Aug-18 10:14:05.239 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (P15053_155) > jobId: 23592206; workDir: /cfs/klemming/projects/supr/uppstore2017202/CSPR/CSPR_nfcore/work/4b/8a46a0aec53ac37c7d5db0fb2766ea Aug-18 10:14:05.240 [Task submitter] INFO nextflow.Session - [4b/8a46a0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (P15053_15 5) Aug-18 10:14:05.284 [Actor Thread 41] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error java.lang.NullPointerException: Cannot get property 'containerEngine' on null object"

Would be very grateful if anyone has any insight what might be going wrong. Thanks you so much!

( I'm the NBIS support that redirected Alice here) The relevant part is

Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX; work-dir=null error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: java.util.LinkedHashMap ([id:P15053_155, strandedness:auto, seq_platform:[], seq_center:[], single_end:false, ha s_genome_bam:false, has_transcriptome_bam:false, original_genome_bam:null, original_transcriptome_bam:null])

specifically

Not a valid path value type

It looks like the pipeline is expecting a path in the input but getting a tuple with a meta map. github.com/nf-core/rnaseq/blob/…/main.nf#… Is this a bug with the pipeline connections?

Looks like it's a problem to do with the strandedness inference pathway, fix incoming. In the meantime, if you know your expected strandedness, set it in the sample sheet rather than using 'auto' and the problem should go away

Than you Mahesh and Jonathan, will try that!

Pipeline-level fix if anyone cares to approve: github.com/nf-core/rnaseq/pull/1907

@Alice Karlsson use

nextflow run nf-core/rnaseq -r dev ...

to run the code with the fix, if you didn't already fix it by specifying strandedness.

Thank you! Yes, specifying the strandedness resolved it too:D