I'm using the pipeline, 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.
Command used and terminal output
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
TERMINAL OUTPUT
Execution cancelled -- 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_RNASPLICE:RNASPLICE:INPUT_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_RNASPLICE:RNASPLICE:INPUT_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
Relevant files
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
Description of the bug
I'm using the pipeline, 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.
Command used and terminal output
Relevant files
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
System information
No response