MissingInputException in rule biomarker_hrd when trying to run this module with Twist_DNA_Solid

[ljmesi]

Check Documentation

I have checked the following places for your error:

• [x] snakemake website: troubleshooting

Description of the bug

When running this module with Twist_DNA_Solid the pipeline fails to run. (I'm not sure if this is the right place to file this bug report here since this is a problem with Twist_DNA_Solid.)

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:

   snakemake --cores 92 \
   --use-singularity \
   --singularity-args "--bind /home/lauri/ --bind /data/" \
   -s /home/lauri/Desktop/Twist_DNA_Solid/workflow/Snakefile

2. See error:

   MissingInputException in line 10 of https://github.com/hydra-genetics/biomarker/raw/develop/workflow/rules/hrd.smk:
   Missing input files for rule biomarker_hrd:
   cnv_sv/cnvkit_call_loh/LI-VAL-09_T.loh.cns

Expected behaviour

Pipeline should have run.

Log files

Have you provided the following extra information/files:

• [x] The command used to run the pipeline

System

• Hardware: Desktop
• Executor: local
• OS: Linux Ubuntu
• Version: 20.04

Snakemake Installation

• Version: 6.10.0

Container engine

• Engine: Singularity
• version: 3.8.5

Additional context

I would guess that in this line: https://github.com/hydra-genetics/biomarker/blob/d5847c71cdcc6573c19fe838540c9114fffd39ab/workflow/rules/hrd.smk#L12 maybe it should be:

        segment="cnv_sv/cnvkit_call/{sample}_{type}.loh.cns",

(I haven't managed to double-check if this the case.)

[jonca79]

Solved!