tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
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pipeline: correct handling of optional run_directory suffix in Paths Sheet #320
Documentation comments in the Paths Sheet indicate that the run_directory suffix is optional. However, if omitted this will produce a processed Run Config that contains relative run directory paths which don’t correctly resolve when cwltool gathers file inputs. This results in the following error when the tinyRNA workflow reaches the tiny-count step:
ERROR Input object failed validation:
[Errno 2] No such file or directory: '[…] /tinyrna_2023-09-10_00-00-00/tinyrna_2023-09-10_00-00-00/run_config.yml'
Documentation comments in the Paths Sheet indicate that the run_directory suffix is optional. However, if omitted this will produce a processed Run Config that contains relative run directory paths which don’t correctly resolve when cwltool gathers file inputs. This results in the following error when the tinyRNA workflow reaches the tiny-count step:
ERROR Input object failed validation: [Errno 2] No such file or directory: '[…] /tinyrna_2023-09-10_00-00-00/tinyrna_2023-09-10_00-00-00/run_config.yml'