Add low biomass pipelines and update standard metagenomics pipeline#197
Open
Add low biomass pipelines and update standard metagenomics pipeline#197
Conversation
Contributor
bnovak32
commented
Apr 15, 2026
bnovak32
commented
- updated standard Illumina Metagenomics pipeline
- replace bbduk with fastp
- add steps that were missing from previous pipeline definition
- two new metagenomics pipelines for low biomass (long-read (Nanopore) and short-read (Illumina))
- includes additional pre-processing steps for read decontamination
- decontamination steps in downstream analysis
- add visualizations and downstream analysis to all pipelines
- update all software packages to latest possible without changing results
- removed read-based processing from standard pipeline (no longer used, humann does not work with this data type)
First draft nanopore low biomass pipeline
* Update to latest draft * Add read-based feature table decontamination steps * Add taxonomy plots * Regularize formatting
Low biomass nanopore metagenomics
1. Fixed bugs with host tar command and the run_decontam R function. 2. Fixed bug with reading and writing species table 3. Fixed bug with running decontam and plotting non-contaminant features.
* Formatting updates * Update step names * Add missing steps * Fix broken links
Fixed a typo in the fasta file name for Mycobacterium marinum.
Fixed typo in metaphlan version specification.
- Updated Long-read document to better match latest workflow
- Added first draft of Short-read document
TODO:
- Fix Assembly-based decontamination and heatmaps
- Finish Short-read document (only revised through pre-processing,
which also requires some overhaul)
- Updated GL-DPPD-7117 to 1st draft status - Fixed some links and formatting in GL-DPPD-7116 TODO: Add barplots and decontamination to read-based metaphlan taxonomies
- started renaming fastq files to move assay suffix to end - fixed typos in the table of contents
- Add missing steps (Read-based metaphlan taxonomies and assembly-based heatmaps) - Fix documentation for kraken2-build (adding references to fasta acquisition) - Update/fix table of contents - Regularize formatting - Fix typos - remove Nanopore specific tools from software table
* Update GL-DPPD-7116.md through step 9c (set global variables). * Fix numbering in GL-DPPD-7116.md
- sync changes between long and short read documents
Sync with working implementation
- fixed spelling/typos across both documents
- Short-read specific updates
- removed remove human reads step and added reference to remove human
reads pipeline
- add Humann output downstream analysis steps
- Long-read specific updates
- Update human read removal to sync with latest human read removal pipeline and add link to that pipeline
- update kraken2 database build steps to use k2 wrapper (as in latest RHR and EHR pipelines/workflows)
- renumbered steps and fixed internal links
- updated thresholds to match latest implementation
- add missing assay suffixes and fix incorrect suffixes
- remove unused samtools index step in Assembly-based processing
- update output file names
- change all csv output to tsv
- updated software tables to remove references to unused software in each pipeline.
- fix broken links
- add missing filtering steps in Assembly-based processing
- Updated header information
- Add top50 heatmaps
- added note about decontaminated plots and species tables only being
present when 1 or more contaminants found
- reorganize R code
- updated Metagenomics READMEs - added Metagenomics workflow submodule for low biomass pipelines - updated low biomass pipeline docs table-of-contents
- updated all numbering - fixed broken link - removed incorrect references to gzipped fasta
- sync the standard metagenomics pipeline doc to the updates in the low biomass pipeline docs. - also fixes some typos found in the low biomass docs
fix document number typo
- Updated software versions to latest possible - Specify separate tidyverse instead of the tidyverse collection for more granular software versions - Add final pipeline approval date
- changed NF_Metagenomics to NF_MetagenomeSeq - updated READMEs
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.