RHR - Updates to Nextflow code#194
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bnovak32 wants to merge 9 commits intonasa:DEV_Metagenomics_rmHR_NF_conversionfrom
Open
RHR - Updates to Nextflow code#194bnovak32 wants to merge 9 commits intonasa:DEV_Metagenomics_rmHR_NF_conversionfrom
bnovak32 wants to merge 9 commits intonasa:DEV_Metagenomics_rmHR_NF_conversionfrom
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bnovak32
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Feb 13, 2026
bnovak32
commented
- added generate_summary script and corresponding compile_summary process in order to correctly sort summary file in same order as input sample ID file
- removed sample tmp files as a published output
- migrated from publishDir to workflow.output for most processes
- updated kraken2 DB build to include other options based on provided input
- added nextflow.schema for input validation and help generation
- update kraken2-build to use k2 wrapper throughout
- started updating protocol text generation to allow passing protocol text from existing kraken2 DB folder
- fixed kraken2 output file gzip and rename procedure
- added generate_summary script and corresponding compile_summary process in order to correctly sort summary file in same order as input sample ID file - removed sample tmp files as a published output - migrated from publishDir to workflow.output for most processes - updated kraken2 DB build to include other options based on provided input - added nextflow.schema for input validation and help generation - update kraken2-build to use k2 wrapper throughout - started updating protocol text generation to allow passing protocol text from existing kraken2 DB folder - fixed kraken2 output file gzip and rename procedure
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…hosts.csv and main.nf for improved workflow handling
- updated pipeline doc and READMEs to specifically talk more about human read removal - updated approver list and date - updated READMes - switched to k2 download-taxonomy - updated kraken2 build db definitions
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