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biowdl / tasks

A collection of reusable WDL tasks. Category:Other
https://biowdl.github.io/tasks/
MIT License
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Add mkdir line to samtools fastq. #280

Closed JasperBoom closed 3 years ago

JasperBoom commented 3 years ago

Checklist

JasperBoom commented 3 years ago

I also adjusted some CHANGELOG entries to address the previous PR 277.

JasperBoom commented 3 years ago

Local tests on SLURM are running without issues. But for some reason the tests on GitHub are producing this error:

 Job SubreadsProcessing.bam2FastqLima:1:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /tmp/pytest_workflow_xuq357ge/dna.fastq/cromwell-executions/SubreadsProcessing/afe35f45-1102-4757-92a8-16f4c757f8fe/call-bam2FastqLima/shard-1/execution/stderr.
 [First 3000 bytes]:>|> 20210614 08:49:31.235 -|- FATAL -|- Run -|- 0x7f0846ccfb80|| -|- bam2fastq ERROR: [pbbam] PBI index I/O ERROR: could not open file for reading:
  file: /cromwell-executions/SubreadsProcessing/afe35f45-1102-4757-92a8-16f4c757f8fe/call-bam2FastqLima/shard-1/execution/batch.1.march.Sample_1_3p--Sample_1_3p.bam.pbi
  reason: No such file or directory

This happens when the .pbi file is not in the same place as the .bam file. I am hoping that cp will do what ln is not doing right now.

JasperBoom commented 3 years ago

Local tests on SLURM are running without issues. But for some reason the tests on GitHub are producing this error:

 Job SubreadsProcessing.bam2FastqLima:1:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /tmp/pytest_workflow_xuq357ge/dna.fastq/cromwell-executions/SubreadsProcessing/afe35f45-1102-4757-92a8-16f4c757f8fe/call-bam2FastqLima/shard-1/execution/stderr.
 [First 3000 bytes]:>|> 20210614 08:49:31.235 -|- FATAL -|- Run -|- 0x7f0846ccfb80|| -|- bam2fastq ERROR: [pbbam] PBI index I/O ERROR: could not open file for reading:
  file: /cromwell-executions/SubreadsProcessing/afe35f45-1102-4757-92a8-16f4c757f8fe/call-bam2FastqLima/shard-1/execution/batch.1.march.Sample_1_3p--Sample_1_3p.bam.pbi
  reason: No such file or directory

This happens when the .pbi file is not in the same place as the .bam file. I am hoping that cp will do what ln is not doing right now.

It seems the PacBio bam2fastx tool is causing too many issues. I have replaced the tool with samtools fastq.