NF_MAAgilent1ch: Update pipeline version from GL-DPPD-7112 to GL-DPPD-7112-A#140
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cyouh95 wants to merge 18 commits intonasa:DEV_NF_MAAgilent_1chfrom
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NF_MAAgilent1ch: Update pipeline version from GL-DPPD-7112 to GL-DPPD-7112-A#140cyouh95 wants to merge 18 commits intonasa:DEV_NF_MAAgilent_1chfrom
cyouh95 wants to merge 18 commits intonasa:DEV_NF_MAAgilent_1chfrom
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- Modified output directory references to use resultsDir (based on accession IDs) instead of outputDir. - Added approach to generate runsheets from user-provided ISA archives. - Updated publishing directories across various processes to align with new structure. - Renamed AGILE1CH process as PROCESS_AGILE1CH - Removed deprecated Agilent array annotations CSV file, and pointed to config.csv inside examples/annotations/ instead - Updated GL-DPPD-7112-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.
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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)