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Fix typo in exportCounts input #350

Merged
merged 3 commits into from
Aug 2, 2022
Merged

Fix typo in exportCounts input #350

merged 3 commits into from
Aug 2, 2022

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schance995
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Rename raw-{dataset} to raw-local-{dataset}. There is no rule that produces raw-{dataset} as output.

This fixes a MissingInputException when running exportCounts without having a populated SPLICE_COUNTS_DIR, such as when using BCM UDN blood samples (https://doi.org/10.5281/zenodo.3963470):

% snakemake -n exportCounts    
WARNING: 64 files missing in samples annotation. Ignoring...
check for missing R packages
MonoallelicExpression has been turned off in the config file
rnaVariantCalling has been turned off in the config file
Structuring dependencies...
Dependencies file generated at: /tmp/tmps8kl_ksp

Building DAG of jobs...
MissingInputException in line 192 of /tmp/tmps8kl_ksp:
Missing input files for rule AberrantSplicing_pipeline_Counting_exportCounts_R:
    output: OutputRev/processed_results/exported_counts/Blood--hg19--gencode34/k_j_counts.tsv.gz, OutputRev/processed_results/exported_counts/Blood--hg19--gencode34/k_theta_counts.tsv.gz, OutputRev/processed_results/exported_counts/Blood--hg19--gencode34/n_psi5_counts.tsv.gz, OutputRev/processed_results/exported_counts/Blood--hg19--gencode34/n_psi3_counts.tsv.gz, OutputRev/processed_results/exported_counts/Blood--hg19--gencode34/n_theta_counts.tsv.gz
    wildcards: dataset=Blood, genomeAssembly=hg19, annotation=gencode34
    affected files:
        OutputRev/processed_data/aberrant_splicing/datasets/savedObjects/raw-Blood/theta.h5	

schance995 and others added 2 commits August 1, 2022 16:06
Rename raw-{dataset} to raw-local-{dataset}. There is no rule that produces raw-{dataset} as output.
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@nickhsmith nickhsmith left a comment

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Thank you for finding this error

@nickhsmith nickhsmith merged commit b45cf0c into gagneurlab:dev Aug 2, 2022
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2 participants