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nf-core / hlatyping

Precision HLA typing from next-generation sequencing data
https://nf-co.re/hlatyping
MIT License
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Getting unbound variable error in optitype(hlatyping) pipeline: Can someone help me #125

Closed varun171 closed 2 years ago

varun171 commented 3 years ago

The exit status of the task that caused the workflow execution to fail was: 1

Error executing process > 'pre_map_hla (1)'

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

Command executed:

yara_mapper -e 3 -t 6 -f bam yara/$baseDir/data/references unzipped_1.fastq unzipped_2.fastq > output.bam samtools view -@ 6 -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam samtools view -@ 6 -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam

Command exit status: 1

Command output: (empty)

Command error: .command.sh: line 2: baseDir: unbound variable

Work dir: /fusion/s3/varun-nextflow-working/scratch/150Rok5sWh0TRL/e8/b54a3bdbe673a4021273dc5cbbab4a

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

christopher-mohr commented 3 years ago

Hi @varun171, which command did you use to start the pipeline?

varun171 commented 3 years ago

Hi Christopher, I used following command. nextflow run 'https://github.com/nf-core/hlatyping' -name hungry_stallman -params-file nf-150Rok5sWh0TRL.params.json -with-tower -r 1.2.0

christopher-mohr commented 3 years ago

It could be this issue. Which Nextflow version are you using?

varun171 commented 3 years ago

I am using 21.04.0 build 5552.

christopher-mohr commented 3 years ago

Would it be possible for you to use Nextflow < 20.04 and check if it works?

christopher-mohr commented 2 years ago

Closed due to lack of feedback.