Trouble running single-ended data

[mancili]

Hi,

I am having trouble running LncPipe for single-end RNA-seq data.

Here is the error message:

Caused by:
  Missing output file(s) `*qc.fq.gz` expected by process `Run_FastP (samplename)`

Command executed:

  fastp -i samplename.fastq.gz -o samplename.qc.gz -h samplename_fastp.html

It seems like the output file from the previous step is named ending with "*.qc.gz", but the process Run_FastP (samplename) looks for files ending with "*qc.fq.gz".

Is it because of this line of code in the main.nf ?

if (params.singleEnd) {
                '''
            fastp -i !{fastq_file[0]} -o !{samplename}.qc.gz -h !{samplename}_fastp.html
           
            '''
            } else {
                '''
            fastp -i !{fastq_file[0]}  -I !{fastq_file[1]} -o !{samplename}_1.qc.fq.gz  -O !{samplename}_2.qc.fq.gz -h !{samplename}_fastp.html
            '''
            }
        }
    }else{
        Channel.fromFilePairs(reads, size: params.singleEnd ? 1 : 2)

Please help!

Thanks,
Manci