File not found during call-gSNP step

[Alfredo-Enrique]

Describe the issue
Metapipeline erros out because file can't be found in call-gSNP step

• Pipeline release version: metapipeline-DNA-5.0.0-rc.4
• SLURM
• F32
  *Submission script
• Actual submission script: /hot/user/alfgonzalez/project/project-LAND-SARC/project-SARC-LAND/pipeline/TCGA-STSA/metapipeline-DNA-5.0.0-rc.4/input/launch_TCGA-STSA_WXS_meta.sh
• Config: /hot/user/alfgonzalez/project/project-LAND-SARC/project-SARC-LAND/pipeline/TCGA-STSA/metapipeline-DNA-5.0.0-rc.4/input/test_TCGA-STSA_WXS_meta.input.config
• Leading work dir: /hot/project/disease/SarcomaTumor/SARC-000118-SarcomaLandscape/data/TCGA-STSA/metapipeline-DNA-5.0.0-rc.4/leading_work_dir
• Logs: /hot/project/disease/SarcomaTumor/SARC-000118-SarcomaLandscape/data/TCGA-STSA/metapipeline-DNA-5.0.0-rc.4/leading_work_dir/1f/f500711d12b1718166b3b79cc040d1/.command.log

To Reproduce
Steps to reproduce the behavior:

1. Go to submission script and config file above
2. Change save location
3. Relaunch launch_TCGA-STSA_WXS_meta.sh

Expected behavior
Gets through align-dna with no issue but gets lost in call-gSNP

Screenshots

Additional context
Name of the output file from aling-DNA: BWA-MEM2-2.2.1_TCGA-STSA_TCGASTSA000001-N001-B01-P
Metapipeline-DNA input sample name: TCGASTSA000001-N001-B01-P

[Alfredo-Enrique]

@yashpatel6 I can patch this if it helps.

Would it be as simple as doing any one of the following? :

1. Rename the output of align-DNA to eliminate underscores?
2. Renaming sm tag in the call-snp input.csv generation? https://github.com/uclahs-cds/metapipeline-DNA/blob/main/module/call_gSNP/create_CSV_call_gSNP.nf#L81-L89
3. Something else: