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NBISweden / GenErode

GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
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snpEff prepare_db_build does not recognize file type #24

Closed verku closed 2 years ago

verku commented 2 years ago 
ImproperOutputException in line 148 of /crex/proj/sllstore2017093/b2016342/b2016342_nobackup/lts/genome_erosion_pipeline/verena_testing/maintenance/issue
s/GenErode/workflow/rules/12_snpEff.smk:
Outputs of incorrect type (directories when expecting files or vice versa). Output directories must be flagged with directory(). for rule prepare_db_buil
d:
/proj/sllstore2017093/b2016342/b2016342_nobackup/lts/genome_erosion_pipeline/verena_testing/development/testdata/gerp/outgroup_Sc9M7eS_2_HRSCAF_41/all_sc
affolds/snpEff/data/GCF_000283155.1_CerSimSim1.0_genomic.Sc9M7eS_2_HRSCAF_41/genes.gtf
verku commented 2 years ago

This error only happens on Rackham. No such error with Github actions (ubuntu) or vm-singularity on Mac.