Hi all ... newbie to nf-core pipelines. Has anybody come across an issue where the test pipeline downloaded and ran successfully without any errors, but gave errors when using it on other datasets? I'm using singularity for software dependencies.

That happened to me once. Had issues with Nextflow environment variables and container caches in my case. Do you mind sending the exact error messages you're getting?

Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: null. The full error message was: Error executing process > 'NFCORE_RNASEQRNASEQFASTQ_QC_TRIM_FILTER_SETSTRANDEDNESSFASTQ SUBSAMPLE FQ SALMONSALMON_INDEX (genome.transcripts.fa)' Caused by: Process

NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa)

terminated for an unknown reason -- Likely it has been terminated by the external system Command executed: if [ -n 'GRCm38.primary_assembly.genome.fa' ]; then grep '^>' GRCm38.primary_assembly.genome.fa | cut -d ' ' -f 1 | cut -d $'\t' -f 1 | sed 's/>//g' > decoys.txt cat genome.transcripts.fa GRCm38.primary_assembly.genome.fa > gentrome.fa fi salmon \ index \ --threads 16 \ -t gentrome.fa \ -d decoys.txt \ --gencode -k 31 \ -i salmon Command exit status: - Command output: Threads = 16 Vertex length = 31 Hash functions = 5 Filter size = 68719476736 Capacity = 2 Files: salmon/ref_k31_fixed.fa -------------------------------------------------------------------------------- Round 0, 0:68719476736 Pass Filling Filtering Command error: [2026-07-31 175315.869] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000226153.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175316.037] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000227002.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175317.705] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000226615.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175318.224] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000229312.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175318.384] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000227223.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175318.985] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000103439.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175318.985] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000103441.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175318.986] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000103739.3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.258] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000165700.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.324] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000180266.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.326] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179262.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.331] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179520.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.331] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000177965.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.336] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178909.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.342] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179883.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.343] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178862.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.356] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178815.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.368] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179793.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.368] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000170385.1], had length less than equal to the k-mer lengthe k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.356] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178815.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.368] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179793.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.368] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000170385.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.369] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179560.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.372] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178811.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.373] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178483.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.375] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000180001.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.377] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178537.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.382] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178549.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.393] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000177564.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.395] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178230.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.396] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000178902.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.398] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179166.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.399] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179932.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.399] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000195858.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.402] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000177839.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.407] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000179664.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.407] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000196221.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.412] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000177646.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.572] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000192089.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.595] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000193012.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.597] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000191703.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175319.710] [puff:index:jointLog] [warning] Entry with header [ENSMUST00000200713.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping) [2026-07-31 175433.481] [puff:index:jointLog] [warning] Removed 1630 transcripts that were sequence duplicates of indexed transcripts. [2026-07-31 175433.481] [puff:index:jointLog] [warning] If you wish to retain duplicate transcripts, please use the

--keepDuplicates

flag [2026-07-31 175436.254] [puff:index:jointLog] [info] Replaced 78088277 non-ATCG nucleotides [2026-07-31 175436.254] [puff:index:jointLog] [info] Clipped poly-A tails from 758 transcripts wrote 141096 cleaned references [2026-07-31 175449.637] [puff:index:jointLog] [info] Filter size not provided; estimating from number of distinct k-mers [2026-07-31 175527.604] [puff:index:jointLog] [info] ntHll estimated 2272627788 distinct k-mers, setting filter size to 2^36 Work dir: /scratch/nfcore_rnaseq_testing/KRAS_SPIB_test/05/38e15b086a8be5600df55d706a9b94 Container: /nfs/nf_core_pipelines/nextflow_singularity_cachedir/depot.galaxyproject.org-singularity-salmon-1.10.3--h6dccd9a_2.img Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named

.command.sh

Looks like the process is being killed by your scheduler rather than by failure inside

SALMON_INDEX

. Seems like it might be an issue of the memory requested not being enough. Maybe update your config file to increase memory for the

SALMON_INDEX

module then resume the existing run:

process {
    withName: '.*:SALMON_INDEX' {
        memory = '128 GB'
        cpus   = 16
        time   = '24h'
    }

Thank you ... I had set those process parameter limits globally (for the resourceLimits option), which is why my pipeline kept crashing out ... Increasing those limits and also additionally setting your suggestion helped resolve the issue .. thanks for your help!