(env_nf) ahmed@ahmed-Precision-5570:~$ nextflow run nf-core/rnasplice --input /home/ahmed/data/mRNA_E_cig/samplesheet.csv --contrasts /home/ahmed/data/mRNA_E_cig/contrastsheet.csv --outdir /home/ahmed/nextflow --genome GRCm38 --skip_alignment --pseudo_aligner salmon -profile docker --max_memory 20.GB Nextflow 24.04.1 is available - Please consider updating your version to it N E X T F L O W ~ version 23.10.1 Launching

<https://github.com/nf-core/rnasplice>

[mad_mccarthy] DSL2 - revision: 1d0494ae34 [master] ------------------------------------------------------ ,--./,-. _ _ _ __ _ /,-._.--~' |\ | |__ _ / ` / \ |_) |__ } { | \| | \__, \__/ | \ |___ \`-._,-

-,

.,.,' nf-core/rnasplice v1.0.4-g1d0494a ------------------------------------------------------ Core Nextflow options revision : master runName : mad_mccarthy containerEngine : docker launchDir : /home/ahmed workDir : /home/ahmed/work projectDir : /home/ahmed/.nextflow/assets/nf-core/rnasplice userName : ahmed profile : docker configFiles : Input/output options input : /home/ahmed/data/mRNA_E_cig/samplesheet.csv contrasts : /home/ahmed/data/mRNA_E_cig/contrastsheet.csv outdir : /home/ahmed/nextflow Reference genome options genome : GRCm38 fasta : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa gtf : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf star_index : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/ igenomes_base : s3://ngi-igenomes/igenomes/ Max job request options max_memory : 20.GB Alignment options aligner : star_salmon skip_alignment : true rMATS options rmats : true DEXSeq DEU options dexseq_exon : true edgeR DEU options edger_exon : true DEXSeq DTU options dexseq_dtu : true min_samps_gene_expr : 4 min_samps_feature_expr: 2 min_samps_feature_prop: 2 Miso sashimi_plot : true miso_genes : ENSG00000004961, ENSG00000005302, ENSG00000147403 miso_genes_file : null !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ suppa.py \ generateEvents \ -i genes.gtf \ -f ioi \ -o events \ -p cat <<-END_VERSIONS > versions.yml "NFCORE_RNASPLICERNASPLICESUPPA_SALMON:GENERATE_EVENTS_IOI": suppa: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('suppa').version)") END_VERSIONS Command exit status: 125 Command output: (empty) Command error: Unable to find image 'quay.io/biocontainers/suppa:2.3--py36_0' locally 2.3--py36_0: Pulling from biocontainers/suppa docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/suppa:2.3--py36_0 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/. See 'docker run --help'. Work dir: /home/ahmed/work/fc/79bff601cb3547cd8edf77be735274 Tip: when you have fixed the problem you can continue the execution adding the option

-resume

to the run command line -- Check '.nextflow.log' file for details (env_nf) ahmed@ahmed-Precision-5570:~$

That's the same error you already reported. It makes it easier for anyone trying to help if all the information stays in one thread. You received a couple of suggestions there -- have you tried anything?