GeneLab_Data_Processing
GeneLab_Data_Processing copied to clipboard
nasa
Changes include: - #85 - #96 - #97 - #99 - #100
Add scripts and a module to perform post-processing tasks like md5sums, readme, file association table, validation and verification and protocol generation.
Existing code in ```RNAseq/Workflow_Documentation/NF_RCP-F/workflow_code/bin/dp_tools__NF_RCP/checks.py```: ```python def check_dge_table_group_columns_constraints( dge_table: Path, runsheet: Path, samples: set[str], **_ ) -> FlagEntry: FLOAT_TOLERANCE = ( 0.001 # Percent allowed difference due to float precision differences...
## Description Numeric sample names cause below error in the following line: ``` TypeError: unsupported operand type(s) for /: 'PosixPath' and 'int' ``` https://github.com/nasa/GeneLab_Data_Processing/blob/90d6bb5d6a20d817fa17ac5cb0763d4f8f75966b/RNAseq/Workflow_Documentation/NF_RCP-F/workflow_code/bin/sort_into_subdirectories_by_sample.py#L26 ## Solution Convert numeric sample names...
- Fix ADD GENE ANNOTATIONS process break when no organism-specific annotation table is used - Improve log2fc VV DGE log entry - Add workflow version to software table - Update...
When running the pipeline from the [DEV_Amplicon_Illumina_NF_conversion](https://github.com/olabiyi/GeneLab_Data_Processing/tree/DEV_Amplicon_Illumina_NF_conversion/Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-C) branch using datasets with multiple assays for the same target (ex. [OSD-417](https://osdr.nasa.gov/bio/repo/data/studies/OSD-417)), it is failing to create a runsheet (at `GET_RUNSHEET` process) with...
TO-DO: - ~Update workflow version~ (updated to 1.0.5) - Check `annotation_config_path` in `default.config` - ~Update Nextflow version~ (updated to 24.10.5)
TO-DO: - ~Update workflow version~ (updated to 1.0.5) - Check `annotation_config_path` in `default.config` - ~Update Nextflow version~ (updated to 24.10.5)
- Renamed "Remove_human_reads_in_raw_data" as "Remove_host_reads" - Created NF_MGRemoveHostReads/ - Updated pipeline doc and workflow documentation
Hi, I am getting an error while running the GTDB step. I am attaching the log file. It seems like Prodigal failed due to an error "AttributeError: module 'numpy' has...
