nf-core / rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
https://nf-co.re/rnasplice
MIT License
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Error single-end execution #130

Closed fcastillo1 closed 7 months ago

fcastillo1 commented 7 months ago

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

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

System information

No response

fcastillo1 commented 7 months ago

The way to solve it was to add the empty fastq_2 column.