Hello everyone. I'm using the nf-core/rnasplice pipeline (https://nf-co.re/rnasplice/dev), but I'm getting an error when trying to run it with my single-end data in the samplesheet file. I wanted to know if anyone has had a similar error and how you solved it please so you can explain it to me. Thank you so much. This is my samplesheet.csv file: sample,fastq_1,strandedness,condition SRR10503052,/home/fcr/proyecto_p1/parte2/SRR10503052_1.fastq.gz,unstranded,BR0 SRR10503053,/home/fcr/proyecto_p1/parte2/SRR10503053_1.fastq.gz,unstranded,BR0 SRR10503054,/home/fcr/proyecto_p1/parte2/SRR10503054_1.fastq.gz,unstranded,BR0 SRR10503095,/home/fcr/proyecto_p1/parte2/SRR10503095_1.fastq.gz,unstranded,BR15 SRR10503096,/home/fcr/proyecto_p1/parte2/SRR10503096_1.fastq.gz,unstranded,BR15 SRR10503097,/home/fcr/proyecto_p1/parte2/SRR10503097_1.fastq.gz,unstranded,BR15 This is the command: nextflow run nf-core/rnasplice --input samplesheet.csv --source fastq --contrasts contrastsheet.csv --outdir /home/fcr/proyecto_p1/parte2/results_RNAsplice4 --genome GRCh37 -profile docker This is the output: OUTPUT TERMINAL Execution canceled -- Finishing pending tasks before exit -[nf-core/rnasplice] Pipeline completed with errors- WARN: The operator

first

is useless when applied to a value channel which returns a single value by definition ERROR ~ Error executing process > 'NFCORE_RNASPLICERNASPLICEINPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)' Caused by: Process

NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)

terminated with an error exit status (1) Command executed: check_samplesheet_fastq.py samplesheet.csv samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "NFCORE_RNASPLICERNASPLICEINPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONS Command exit status: 1 Command output: (empty) Command error: [CRITICAL] The sample sheet must contain these column headers: strandedness, fastq_2, sample, condition, fastq_1. Work dir: /home/fcr/proyecto_p1/parte2/work/12/d830cb6b9c9f0807c2a5da281ea1ad Tip: you can replicate the issue by changing to the process work dir and entering the command

bash .command.run

-- Check '.nextflow.log' file for details

Your sample sheet does not have a

fastq_2

column. Not sure if it can be empty, but it has to be there.

I left it empty and it worked. Thank you.