Dev aina#1
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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.
Updated GBS workflow input descriptions with typical STACKS filenames and clarified expected input files across workflow steps.
Consolidated Galaxy help, support, and contact resources into a dedicated Help and Contact section. Added links for Galaxy Training Network, AGRF support, and Galaxy Australia resources.
Removed duplicated help content from the Import Data section. Kept upload and file compression guidance only to simplify the section structure.
Updated intro navigation links and simplified footer content. Removed unused placeholder logos, extra contact links, and contributor display content for a cleaner interface.
Removed the previous help.yml section and deleted unused contributor content. Updated section references in base.yml to use the new Help and Contact section.
Updated base.yml configuration files to replace the old help section reference with the new Help and Contact section.
Updated microbial profiling tool descriptions to better explain tool functionality, expected outputs, and common output file formats. Added clearer user-friendly descriptions for diversity analysis, taxonomy visualisation, ordination, differential abundance, functional prediction, sequence alignment, and phylogenetic analysis tools.
Updated RNA-seq tool descriptions to explain each tool’s purpose, expected outputs, and common output file formats. Improved clarity for QC, trimming, alignment, quantification, filtering, normalisation, differential expression, and visualisation tools.
Updated microbial profiling descriptions, outputs, and datatype information for improved clarity and user guidance.
Updated metagenomics workflow descriptions, outputs, and datatype information for improved clarity, consistency, and user guidance.
Updated GBS workflow descriptions, outputs, and datatype information for improved clarity, consistency, and user guidance.
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Currently there is a part of the quality control section that refers to a non-existent (or not shared with us) workflow, pointing to |
Same with the PacBio data part of the qc section. |
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The quality control section could benefit from a slight revision:
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Updated the Sequencing Quality Control section based on review feedback. Removed broken workflow references, added NanoPlot, MultiQC, and Cutadapt tools, improved descriptions and outputs, added labelled input datatypes, and revised overview text for better clarity and consistency.
Updated metagenomics tool descriptions to better explain tool functionality, expected outputs, and common output file formats. Improved user-friendly descriptions for assembly, assembly quality assessment, taxonomic classification, genome binning, genome quality assessment, and functional annotation workflows.
Updated GBS workflow tool descriptions to better explain tool functionality, expected outputs, and common output file formats. Improved user-friendly descriptions for STACKS population genomics workflow tools including locus assembly, catalogue generation, SNP calling, genotype analysis, and variant filtering.
Updated the Import Data section with clearer and more user-friendly instructions for uploading and compressing sequencing files in Galaxy. Improved formatting, terminology, and guidance for FASTQ/FASTA file handling and added a working Galaxy compression tool link.
Updated the Quality Control section with clearer and more user-friendly descriptions for Illumina and PacBio quality control workflows. Improved explanations for FastQC, FastP, format conversion, and HiFi quality control workflows, including expected outputs and common output file formats.
Added a prominent notice to the AGRF Galaxy Lab landing page clarifying that the site provides self-serve Galaxy tools and training resources. The notice directs users to Galaxy Australia for platform and tool support, and to AGRF for complex bioinformatics analyses and service enquiries.
Renamed Microbial section to Microbial Profiling, updated overview content to describe both short-read and long-read microbial profiling approaches, and replaced workflow endorsement with guidance directing workflow support requests to Galaxy Australia.
Applied review feedback to the Microbial Profiling and Sequencing Quality Control sections, including workflow support guidance, PacBio QC simplification, SmartLink notes, and updated short-read/long-read descriptions.
Updated the Metagenomics section by separating short-read and long-read assembly tools. Added dedicated sections for MEGAHIT and metaSPAdes (short-read assembly) and meta-hifiasm (long-read assembly) to improve clarity and better reflect different sequencing approaches.
Removed workflow support content and updated microbial section structure.
Added Genome Assembly card and updated homepage navigation links.
Added Genome Assembly section to the AGRF Lab navigation and section list.
Added a new Genome Assembly section including overview, tools, and tutorials. Added support for SPAdes, hifiasm, QUAST, BUSCO, Bakta, FastANI, and MUMmer.
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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.