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Problem While running balsamic config case ....... Problems calling delly_exclusion_converted from the reference JSON.
balsamic config case ......
delly_exclusion_converted
Error message
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
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",
"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
The text was updated successfully, but these errors were encountered:
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Problem
While running
balsamic config case ......
. Problems callingdelly_exclusion_converted
from the reference JSON.Error message
Commands to reproduce
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
The text was updated successfully, but these errors were encountered: