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Fixed a couple of spelling mistakes and moved the location of base.yml, since the local rendering expected it under static/local
Added a file to gitignore
Added QIIME2 Principal Coordinates Analysis (PCoA) tool
Added tool entry for qiime2 feature-table summarize with inputs and Galaxy tool link.
Added Krona tool entry under visualization tools for interactive taxonomic visualization in microbial profiling section.
Heatmaps show feature abundance across samples, while taxonomy bar plots show the relative abundance of taxa in each sample.
Added PICRUSt2 tool for predicting microbial functions in the microbial tools section.
Added qiime2 feature-table filter-samples tool to enable metadata-based filtering (e.g., group exclusion and outlier removal) in the PacBio 16S workflow.
Added RNASeq workflow section to the AGRF lab page. Updated intro.md grid layout to include RNASeq navigation button. Updated base.yml to load rnaseq.yml section.
Added rnaseq.yml with initial structure including overview and tools sections. Includes alignment, differential expression, and visualisation tools. Further details on input/output files will be added.
Added RNASeq tools including quality control (FastQC, MultiQC) and alignment (STAR).
Added gene quantification step using featureCounts to convert aligned reads into count matrices for downstream differential expression analysis.
Added filtering section including sample filtering and low count gene filtering to improve downstream differential expression analysis.
Added normalization section to explain adjustment of sequencing depth and library size.
very few corrections
Added input file details (FASTQ, FASTA, GTF) for STAR alignment step in RNASeq workflow.
Added required inputs for differential expression analysis tools.
Created metagenomics.yml and added initial assembly tools (MEGAHIT, metaSPAdes/meta-hifiasm). Linked section in base.yml and homepage.
Added metagenomics workflow including assembly and assembly QC.
Added MetaBAT binning with inputs.
Added MetaBAT for binning contigs into genome bins based on coverage and composition.
Added GTDB-Tk for assigning taxonomy to genome bins.
Added assembly, QC, binning, binning QC, and taxonomy steps with inputs, outputs, and Galaxy tool links.
Added Galaxy tool links (FastQC, MultiQC, STAR, featureCounts, edgeR, DESeq2) and defined inputs for core analysis steps.
Updated RNA-seq workflow by removing PCA tool link and refining visualization steps. Ensured correct inputs, outputs, and tool links for all sections.
Updated metagenomics workflow by refining descriptions, adding inputs , and improving tool clarity. Ensured alignment with standard assembly, binning, QC, and taxonomy steps.
Updated microbial profiling workflow by correcting tool links, fixing beta diversity steps, and improving overall structure and clarity.
Implemented microbial (16S) workflow including alpha and beta diversity analysis, ANCOM for differential abundance, PICRUSt2 for functional prediction, and visualization tools such as Krona, heatmaps, and taxonomy barplots.
Removes adapters, low-quality base and produces clean FASTQ reads for alignment
Filters out ribosomal RNA to retain clean reads for alignment.
Sorts BAM files, organizes aligned reads by genomic position for downstream analysis.
Assembles transcripts from RNA-seq data, estimates gene expression from aligned reads.
…opulations. This workflow processes sequencing data to build loci, create a catalog, match samples, convert data, call SNPs, and generate population statistics.
Added a tutorial section in the RNASeq module with a link to Galaxy Training Network transcriptomics resources. This provides users with access to RNASeq tutorials and learning materials for analysis workflows.
Added concise inline descriptions to RNASeq tools using title_md for better readability Updated multiple tools for consistency and clarity Maintained detailed explanations using description_md
Added concise inline descriptions to metagenomics tools for better readability and consistency.
Created a new GBS section including Overview, Tools, and Tutorials tabs. Added STACKS workflow tools with descriptions, inputs, outputs, and Galaxy tool links. Included variant analysis tutorials from the Galaxy Training Network.
Added GBS section into intro
Implemented a new "Learn Galaxy" section in the AGRF Lab interface to guide users toward relevant training and documentation resources. The section includes curated links to Galaxy Training Network tutorials covering: - Variant analysis (including GBS workflows) - Microbiome analysis - RNA-seq workflows - Metagenomics pipelines - Population genomics approaches Also added links to official Galaxy documentation for additional support. This enhancement improves usability by helping users understand and apply Galaxy tools and workflows effectively.
Replaced placeholder text with a clear description of microbiome analysis workflows in Galaxy, including diversity analysis and taxonomy.
Replaced placeholder text with a brief description of RNA-seq workflows, including alignment and differential expression analysis.
Updated the description to better explain metagenomics workflows such as classification, assembly, and analysis in Galaxy.
Added Bakta for functional annotation of metagenomic assemblies.
Added key QIIME2 tools to the microbial (16S) analysis section. - Added MAFFT for multiple sequence alignment - Added BLAST (feature-classifier) for taxonomic classification - Added FastTree for phylogenetic tree construction Updated button links to use correct Galaxy tool IDs and removed version-specific URLs for consistency. Ensured proper placement under the tools section and verified rendering locally.
added gbs into base.yml
Added complete RNASeq overview section including workflow description, results, and file outputs. Structured content to match microbial section with clear categories for raw data, QC, alignment, quantification, differential expression, and visualisation. Improved clarity and consistency of file descriptions and formats.
Added the Metagenomics section to the AGRF Lab page, including: - Overview of metagenomics workflow (assembly, binning, annotation) - Structured “Results include” section - Clean “What files are included” table for output files - File formats used for downstream analysis Improved formatting for consistency with existing microbial section.
…utputs Implemented GBS overview section including service description, expected results, file outputs, and file format definitions. Structured content to align with microbial and metagenomics sections for consistency.
Improved RNA-seq section by standardising terminology, refining file naming conventions, and enhancing clarity of output descriptions to maintain consistency across all AGRF lab sections.
Added GBS workflow tools (Stacks pipeline) and integrated bcftools filtering for VCF reanalysis. Updated outputs and file format sections to reflect NGSEP-based results and downstream analysis steps.
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Added QIIME2 Principal Coordinates Analysis (PCoA) tool to the microbial.yml beta diversity section. This tool generates PCoA plots from beta diversity distance matrices to visualize relationships between microbial communities.