NF_MAAffymetrix: Update pipeline version from GL-DPPD-7114 to GL-DPPD-7114-A - #137
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NF_MAAffymetrix: Update pipeline version from GL-DPPD-7114 to GL-DPPD-7114-A#137cyouh95 wants to merge 35 commits into
cyouh95 wants to merge 35 commits into
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This reverts commit d07ee40.
- Update pipeline doc header - Add missing bioconductor/tidyverse software info - update bioconductor to correct version throughout document - fix dp_tools command to use plugin and point to workflow code for plugin example - add optional URL/date columns to annotation file readme - update links throughout both documents to point to absolute paths for anything outside of the Affymetrix folder
…ses, and enhance annotation handling - Removed deprecated Affymetrix array annotations CSV file, and pointed to config.csv inside examples/annotations/ instead - Updated GL-DPPD-7114-A documentation to reflect changes and software versions. - Improved software version tracking in CHANGELOG and README files. - Applied fixes to convert figshare ndownloader URLs to direct API endpoints. - Simplified group sample retrieval in differential expression analysis. - Adjusted workflow scripts to publish runsheets and ISA archives correctly. - Updated software dependencies and their respective versions in the workflow configuration. - Improved clarity in protocol generation and documentation.
…o run in runsheet mode
…es and versions in documentation and configuration files, update CHANGELOG.md
…tp-dump, nf-schema support, misc. changes - Added STAGE_ANALYSIS subworkflow (GET_ACCESSIONS/FETCH_ISA/ISA_TO_RUNSHEET -> PARSE_RUNSHEET -> COPY_ARRAY_DATA_FILES): stages and decompresses all array data files via Nextflow before analysis - Added parse_runsheet.nf for runsheet parsing/validation - Updated default.config with new accession/API params; DUMP_META, GENERATE_SOFTWARE_TABLE, VV_AGILE1CH now use dynamic output directories - Replaced live biomaRt::getBM() queries in the QMD with direct downloads of Ensembl's FTP mart-dump tables; drop chunking/retry/Sys.sleep tied to those queries - Removed redundant biomaRt "not used" block from versions output and added conditional reporting of purrr - Updated sotware_versions and protocol generation to comply with these changes - Added nextflow schema support for parameter validation and help text - Switched to parameterized protocol creation (instead of hard-coding versions, etc.) - Added conda support for easier local development/debugging - Moved protocol creation from post-processing to main nextflow script to make passing needed values easier/more robust - Renamed `annotation_config_path` as `array_annot_path` and `config.csv` as `design_info.csv` throughout - Add `create_date` to design_info.csv and parse it in the protocol
- Resolved output directory to mirror its handling in main's stage-analysis - Replaced dp_tools dependency in ISA table update and md5sum table generation with standalone scripts - Added new PURGE_PROCESSING_INFO Nextflow module to strip full paths from array_annot_path in processing_info.txt before publishing - Added parameter validation and summary log from nf-schema
- Renamed module files from UPPERCASE.nf to lowercase.nf following Nextflow community convention - Flattened directory-based modules (PROCESS_NAME/ with scripts under resources/usr/bin/) to single lowercase process_name.nf files directly under modules/ - Moved process scripts from modules/PROCESS_NAME/resources/usr/bin/ to the top-level bin/ directory
… license table, and remove unused package licenses
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TO-DO:
Update workflow version(updated to 1.0.5)annotation_config_pathindefault.configUpdate Nextflow version(updated to 24.10.5)