Error executing process > 'CHECK_SAMPLE_SHEET (1)'

[AaronHY]

To whom may concern,

Thanks for such a nice workflow. I have tried to use it and there comes some error regarding the "CHECK_SMAPLE_SHEET" as below. I used the suggested python script to make the sample.csv. Could you please help with it?

Script

nextflow run peterk87/nf-iav-illumina --input samplesheet1.csv -profile singularity

samplesheet1.csv

sample,fastq_1,fastq_2 1,/mnt/e/labwork/flu/testraw/1_S1_L001_R1_001.fastq.gz,/mnt/e/labwork/flu/testraw/1_S1_L001_R2_001.fastq.gz 2,/mnt/e/labwork/flu/testraw/2_S2_L001_R1_001.fastq.gz,/mnt/e/labwork/flu/testraw/2_S2_L001_R2_001.fastq.gz 3,/mnt/e/labwork/flu/testraw/3_S3_L001_R1_001.fastq.gz,/mnt/e/labwork/flu/testraw/3_S3_L001_R2_001.fastq.gz 4,/mnt/e/labwork/flu/testraw/4_S4_L001_R1_001.fastq.gz,/mnt/e/labwork/flu/testraw/4_S4_L001_R2_001.fastq.gz 5,/mnt/e/labwork/flu/testraw/5_S5_L001_R1_001.fastq.gz,/mnt/e/labwork/flu/testraw/5_S5_L001_R2_001.fastq.gz

Output

Error executing process > 'CHECK_SAMPLE_SHEET (1)'

Caused by: Process CHECK_SAMPLE_SHEET (1) terminated with an error exit status (127)

Command executed:

check_sample_sheet.py samplesheet1.csv samplesheet.fixed.csv

Command exit status: 127

Command output: (empty)

Command error: /bin/bash: line 0: cd: /mnt/e/labwork/flu/test/work/40/3c36e6e9608c400ad5323d65db3cfe: No such file or directory /bin/bash: .command.run: No such file or directory

Work dir: /mnt/e/labwork/flu/test/work/40/3c36e6e9608c400ad5323d65db3cfe

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[peterk87]

Hi @AaronHY we recently identified and fixed an issue with the Singularity profile. If that profile is still not working, please let us know.

Have you tried the Conda profile?