Closed GimenaA closed 6 months ago
I'm also running into the same issue! I thought it was the minimum sample/feature tags, so I set it to zero: min_samps_gene_expr: 0 min_gene_expr: 0 min_samps_feature_expr: 0 min_feature_expr: 0 min_samps_feature_prop: 0 min_feature_prop: 0 That wasn't the issue either, so I'm hoping someone knows how to solve this.
Hey @GimenaA
Thanks for reporting your issue. Can you please try with the latest release? I have a feeling you are using an older version where we didn't handle sample names with dashes in them correctly. See this PR for details.
Closing as completed. Please re-open if you are still facing the same issue.
Description of the bug
I'm getting an error with DRIMSeq when I try to run rnasplice. The pipeline works fine with other samples, so I'm not sure what's causing this error.
Command used and terminal output
Relevant files
Samplesheet file: sample,fastq_1,fastq_2,strandedness,condition ID11-IP-Arc-R2,/path/to/rawdata/ID11-IP-Arc-R2_1.fastq.gz,/path/to/rawdata/ID11-IP-Arc-R2_2.fastq.gz,unstranded,treatment IP-Arc-R1,/path/to/rawdata/IP-Arc-R1_1.fastq.gz,/path/to/rawdata/IP-Arc-R1_2.fastq.gz,unstranded,treatment ID-2-Arc-IP-R3,/path/to/rawdata/ID-2-Arc-IP-R3_1.fastq.gz,/path/to/rawdata/ID-2-Arc-IP-R3_2.fastq.gz,unstranded,treatment ID-5-Non-IP-R3,/path/to/rawdata/ID-5-Non-IP-R3_1.fastq.gz,/path/to/rawdata/ID-5-Non-IP-R3_2.fastq.gz,unstranded,Control ID12-Non-Arc-R2,/path/to/rawdata/ID12-Non-Arc-R2_1.fastq.gz,/path/to/rawdata/ID12-Non-Arc-R2_2.fastq.gz,unstranded,Control Non-Arc-R1,/path/to/rawdata/Non-Arc-R1_1.fastq.gz,/path/to/rawdata/Non-Arc-R1_2.fastq.gz,unstranded,Control
params.yaml file: input: '/path/to/sequencing_data/Arc_RIPseq-samplesheet.csv' contrasts: '/path/to/sequencing_data/Arc_RIPseq-contrastsheet.csv' outdir: '/path/to/sequencing_data/' fasta: '/home/gimena/reference_files/BDGP6.32_ensemble/Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa' gtf: '/home/gimena/reference_files/GTF_files/fromEnsembl/Drosophila_melanogaster.BDGP6.32.106.gtf' source: 'fastq' aligner: 'star_salmon' min_samps_gene_expr: 6 min_gene_expr: 10 min_samps_feature_expr: 3 min_feature_expr: 10 min_samps_feature_prop: 3 min_feature_prop: 0.1 sashimi_plot: true fig_height: 20 fig_width: 20 miso_genes: FBgn0265487 skip_bigwig: false dexseq_dtu: true suppa: false edger_exon: false dexseq_exon: false rmats: false
System information
Nextflow Version: version 23.10.0 Linux OS Version of nf-core/rnasplice 1.0.1