[BUG] Sentieon_BQSR is not skipped when dbsnp and indel files are not provided

[grendon]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/sarek pipeline documentation

Description of the bug

I want the sarek pipeline to SKIP BQRS because I don't have dbsnp and indels for my rice genome. But the pipeline tries to run Sentieon_BQSR anyway and fails. What am I doing wrong?

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:

nextflow run ./sarek/ -c mapping.conf -profile uiuc_hpcbio --custom_config_base /home/groups/hpcbio/projects/meksem/2021-June-Rice/results/20210612-11-Samples/configs -resume -qs 4 -with-report -with-trace

2. See error:

Meksem_8.deduped.bam`         --algo QualCal         -k input.3         Meksem_8.recal.table

  sentieon driver         -t 24         -r GCF_001433935.1_IRGSP-1.0_genomic.fna         -i Meksem_8.deduped.bam         -q Meksem_8.recal.table         --algo QualCal         -k input.3         Meksem_8.table.post         --algo ReadWriter Meksem_8.recal.bam

  sentieon driver         -t 24         --algo QualCal         --plot         --before Meksem_8.recal.table         --after Meksem_8.table.post         Meksem_8_recal_result.csv

Command exit status:
  1

Command output:
  (empty)

Command error:
  cmdline: /home/apps/software/sentieon/201911/libexec/driver -t 24 -r GCF_001433935.1_IRGSP-1.0_genomic.fna -i Meksem_8.deduped.bam --algo QualCal -k input.3 Meksem_8.recal.table
  This software is licensed to dslater@illinois.edu by Sentieon Inc.
  Error: Unrecognized format for vcf file input.3

Work dir:
  /home/groups/hpcbio/projects/meksem/2021-June-Rice/results/20210612-11-Samples/work/e0/62a1cb946b94d27021fa2333f8cdc5

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Expected behaviour

I expected the pipieline to skip the Sentieon_BQSR process where it failed

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

nextflow.log
samples.tsv.txt
mapping.conf.txt

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

nextflow/20.11.0-edge-Java_1.8.0_152

Container engine

• Engine: singularity
• version: 3.4.1
• Image tag: nf-core-sarek-2.7

Additional context

Processing a non-human genome that does not have dbsnp or indel files

[maxulysse]

Hi @grendon

First congratulations, we don't have many people running Sentieon with sarek.
I'm always happy to see other people do it.
Unfortunately, the small number of people using this feature should explain why it's failing for you at the moment.
I added Sentieon for clinical purpose, so I haven't taken into account the possibility of not having dbsnp and indels.
But I'll make sure to correct that for DSL2.
We currently refactoring sarek for the 3.0 release which will be more modular, and the plan is to fully use this Nextflow functionality with dedicated subworkflows.

[FriederikeHanssen]

@asp8200 How is this handeled currently? Is this issue still relevant?

[asp8200]

This is issue no longer relevant as we don't have Sentieon's BQSR function implemented in Sarek, and we don't plan to implement it in Sarek.

https://github.com/nf-core/sarek/blob/dev/docs/usage.md#qualcal-bqsr