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[ Failed Analysis ] problem with balsamic config generation #704

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ashwini06 opened this issue Aug 13, 2021 · 0 comments · Fixed by #705
Closed

[ Failed Analysis ] problem with balsamic config generation #704

ashwini06 opened this issue Aug 13, 2021 · 0 comments · Fixed by #705
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Bug Something isn't working

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@ashwini06
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Problem
While running balsamic config case ....... Problems calling delly_exclusion_converted from the reference JSON.

Error message

a1

Commands to reproduce

fastq_dir='/home/proj/production/cancer/cases'
analysis_dir='/home/proj/production/cancer/github_issue_analysis/issue_40/analysis_APJ/'
balsamic_cache='/home/proj/long-term-stage/cancer/UMI_analysis_runs_APJ/balsamic_test_cache/'
target_panel='/home/proj/production/cancer/reference/target_capture_bed/production/balsamic/gmcksolid_4.1_hg19_design.bed'

balsamic config case -p $target_panel -t $fastq_dir/$caseid/fastq/concatenated_*_XXXXXX_R_1.fastq.gz --case-id $caseid --analysis-dir $analysis_dir --balsamic-cache $balsamic_cache

If workflow, which rules
BALSAMIC/workflows/reference.smk

Solution
Wrong spacing issue:
"delly_exclusion_converted ": "/home/proj/long-term-stage/cancer/UMI_analysis_runs_APJ/balsamic_test_cache/7.2.6/hg19/genome/delly_exclusion_converted.tsv",

Version (please complete the following information):
7.2.6

@ashwini06 ashwini06 added Bug Something isn't working Failed Analysis labels Aug 13, 2021
@ashwini06 ashwini06 linked a pull request Aug 13, 2021 that will close this issue
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@hassanfa hassanfa mentioned this issue Aug 25, 2021
8 tasks
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