From 6caa409f1d6f553f1619e72fc47525cf6a9d28ea Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Feb 2026 17:38:15 -0400 Subject: [PATCH 01/51] Fixed spelling and local rendering issue Fixed a couple of spelling mistakes and moved the location of base.yml, since the local rendering expected it under static/local --- agrf/sections/microbial.yml | 3 ++- agrf/{ => static/local}/base.yml | 0 2 files changed, 2 insertions(+), 1 deletion(-) rename agrf/{ => static/local}/base.yml (100%) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 6a9d7d0..4d69c10 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -34,7 +34,7 @@ tabs: - title_md: What files are included? description_md: | - | Fileanme | Description | + | Filename | Description | | -------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | **Raw Data** | | | Demultiplexed \*.FASTQ file (1 file per sample) | Contains sequencing reads for each sample | @@ -400,3 +400,4 @@ tabs: # description_md: Contact AGRF for more help with your data. # button_md: Contact AGRF # button_link: /request/support + diff --git a/agrf/base.yml b/agrf/static/local/base.yml similarity index 100% rename from agrf/base.yml rename to agrf/static/local/base.yml From 44dfaf5b2c592a858b6d44bf7709b59a732750f4 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Feb 2026 17:38:48 -0400 Subject: [PATCH 02/51] Added a file to gitignore Added a file to gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..62a5f74 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +python-3.14.3-amd64 (1).exe From b109fcb97eeb206c819767754df61c14fb869c34 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 6 Mar 2026 16:36:47 -0400 Subject: [PATCH 03/51] Add QIIME2 PCoA tool to beta diversity section Added QIIME2 Principal Coordinates Analysis (PCoA) tool --- agrf/sections/microbial.yml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 4d69c10..912ca99 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -303,7 +303,7 @@ tabs: - label: QIIME 2 Artifact file - FeatureTable[Frequency] datatypes: - qza - + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha%2Fqiime2__diversity__alpha" @@ -335,8 +335,6 @@ tabs: datatypes: - qza - tsv - - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_correlation%2Fqiime2__diversity__alpha_correlation" @@ -354,7 +352,18 @@ tabs: - tsv button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_group_significance%2Fqiime2__diversity__alpha_group_significance" + + - title_md: qiime2 diversity pcoa - Principal coordinates analysis + description_md: | + Perform principal coordinates analysis (PCoA) on a beta diversity distance matrix to visualize the relationships between samples in a reduced dimensional space. + inputs: + - label: QIIME 2 Artifact file - Distance Matrix + datatypes: + - qza + + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__pcoa%2Fqiime2__diversity__pcoa" + - title_md: qiime2 diversity beta-rarefaction - Assess sequencing depth sufficiency description_md: | QIIME 2 repeatedly subsamples (rarefies) each sample’s sequence data at different depths (e.g., 1000, 2000, 3000 reads, etc.). From a725e8b247b173c5eeb58010dd070b7f32b56fb0 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 12 Mar 2026 20:47:12 -0400 Subject: [PATCH 04/51] Add QIIME2 feature-table summarize tool to microbial section Added tool entry for qiime2 feature-table summarize with inputs and Galaxy tool link. --- agrf/sections/microbial.yml | 10 ++++++++++ agrf/static/local/base.yml | 2 +- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 912ca99..4fb1fa3 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -132,6 +132,16 @@ tabs: button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2_core__tools__export%2Fqiime2_core__tools__export" + + - title_md: qiime2 feature-table summarize - Summarize feature table + description_md: | + Generate a summary of a feature table, including counts per sample and feature frequency distribution. + inputs: + - label: QIIME 2 Artifact file - FeatureTable[Frequency] + datatypes: + - qza + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__summarize%2Fqiime2__feature_table__summarize" + - title_md: QIIME vizualisation extractor - Visualise .qzv files in Galaxy. description_md: | Use this tool to visualisae .qzv files within Galaxy. diff --git a/agrf/static/local/base.yml b/agrf/static/local/base.yml index d0a068b..62c23d1 100644 --- a/agrf/static/local/base.yml +++ b/agrf/static/local/base.yml @@ -5,7 +5,7 @@ site_name: "Australia" lab_name: AGRF Lab #this will be in caps, at right of logo #or: use the word lab, in same font as agrf logo -galaxy_base_url: https://agrf.usegalaxy.org.au +galaxy_base_url: https://usegalaxy.org.au subdomain: agrf root_domain: usegalaxy.org.au From 114ec2c32979306442dd269140d1f6857dc960c2 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 13 Mar 2026 10:28:23 -0400 Subject: [PATCH 05/51] Add Krona visualization tool Added Krona tool entry under visualization tools for interactive taxonomic visualization in microbial profiling section. --- agrf/sections/microbial.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 4fb1fa3..4fd71eb 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -389,7 +389,15 @@ tabs: button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_rarefaction%2Fqiime2__diversity__alpha_rarefaction" - + - title_md: Krona - Interactive taxonomic visualisation + description_md: | + Krona generates interactive hierarchical visualisations of taxonomic abundance. + inputs: + - label: Taxonomy classification table + datatypes: + - tsv + - biom + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsaskia-hiltemann%2Fkrona_text%2Fkrona-text" From 56dd0b25513c5bab23764d632a24c286c61dc41c Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 13 Mar 2026 12:16:24 -0400 Subject: [PATCH 06/51] Visualise microbial abundance using heatmaps and taxonomy bar plots Heatmaps show feature abundance across samples, while taxonomy bar plots show the relative abundance of taxa in each sample. --- agrf/sections/microbial.yml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 4fd71eb..bd78dad 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -399,6 +399,32 @@ tabs: - biom button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsaskia-hiltemann%2Fkrona_text%2Fkrona-text" + - title_md: qiime2 feature-table heatmap - Visualise feature abundance as a heatmap + description_md: | + Generate a heatmap representation of a feature table to visualise abundance patterns across samples. + inputs: + - label: QIIME 2 Artifact file - FeatureTable[Frequency] + datatypes: + - qza + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__heatmap%2Fqiime2__feature_table__heatmap" + + + + - title_md: qiime2 taxa barplot - Visualise taxonomic composition + description_md: | + Generate interactive stacked bar plots showing the relative abundance of taxa across samples. + inputs: + - label: Feature table with taxonomy + datatypes: + - qza + - label: Taxonomy assignments + datatypes: + - qza + - label: sample metadata + datatypes: + - tsv + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__taxa__barplot%2Fqiime2__taxa__barplot" + - id: tutorials From 5681040b1ad0cfa119b3c5485aa825b9cfcfe91a Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 13 Mar 2026 12:44:12 -0400 Subject: [PATCH 07/51] added picrust2(functional annotation Added PICRUSt2 tool for predicting microbial functions in the microbial tools section. --- agrf/sections/microbial.yml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index bd78dad..6361846 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -389,6 +389,15 @@ tabs: button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_rarefaction%2Fqiime2__diversity__alpha_rarefaction" + - title_md: PICRUSt2 metagenome prediction - Predict microbial functions + description_md: | + Predict microbial functional profiles such as gene families and metabolic pathways from microbial community data. + inputs: + - label: Sequence abundance table (OTUs or ASVs) + datatypes: + - biom + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpicrust2_metagenome_pipeline%2Fpicrust2_metagenome_pipeline" + - title_md: Krona - Interactive taxonomic visualisation description_md: | Krona generates interactive hierarchical visualisations of taxonomic abundance. From 090d6f3949d4b2fcbbcd2334e91bdd64fed99a7b Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 13 Mar 2026 13:47:32 -0400 Subject: [PATCH 08/51] Add metadata filtering tool Added qiime2 feature-table filter-samples tool to enable metadata-based filtering (e.g., group exclusion and outlier removal) in the PacBio 16S workflow. --- agrf/sections/microbial.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 6361846..ae214be 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -164,6 +164,19 @@ tabs: view_tip: View in QIIME2 + - title_md: qiime2 feature-table filter-samples - Filter samples using metadata + description_md: | + Remove samples from a feature table based on sample metadata. + This can be used to exclude groups or remove outlier samples before downstream analysis. + inputs: + - label: QIIME 2 Artifact file - FeatureTable[Frequency] + datatypes: + - qza + - label: sample metadata + datatypes: + - tsv + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__filter_samples%2Fqiime2__feature_table__filter_samples" + - id: alpha_diversity title: Alpha Diversity From c4a13b5d4d7ebe6b4adcce3cca20cfd1efed0256 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 13 Mar 2026 14:39:14 -0400 Subject: [PATCH 09/51] Add RNASeq section and update intro grid layout 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. --- agrf/static/local/base.yml | 1 + agrf/templates/intro.md | 5 ++++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/agrf/static/local/base.yml b/agrf/static/local/base.yml index 62c23d1..0ba1fbf 100644 --- a/agrf/static/local/base.yml +++ b/agrf/static/local/base.yml @@ -26,6 +26,7 @@ sections: - sections/data.yml - sections/qualitycontrol.yml - sections/microbial.yml + - sections/rnaseq.yml # - sections/moreanalysis.yml - sections/learn.yml # - sections/help.yml diff --git a/agrf/templates/intro.md b/agrf/templates/intro.md index 38dd504..85dcf19 100644 --- a/agrf/templates/intro.md +++ b/agrf/templates/intro.md @@ -68,14 +68,17 @@ then add Section, so data becomes dataSection
Microbial Profiling
- +
+
RNASeq
+
Learn Galaxy
Galaxy Help
+
Contact AGRF
From e716ae921c7cc74effb1ba4aa29a999aaaba47c0 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 13 Mar 2026 15:21:40 -0400 Subject: [PATCH 10/51] Updated gitignore --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitignore b/.gitignore index 62a5f74..921816b 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,5 @@ python-3.14.3-amd64 (1).exe +venv +venv311 +.DS_Stores +agrf/base.yml \ No newline at end of file From b6fd5d15ab8cec5f099aa180d2fa2dc833be2e01 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Wed, 18 Mar 2026 18:16:36 -0400 Subject: [PATCH 11/51] Add RNASeq 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. --- agrf/sections/rnaseq.yml | 52 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 agrf/sections/rnaseq.yml diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml new file mode 100644 index 0000000..f47b335 --- /dev/null +++ b/agrf/sections/rnaseq.yml @@ -0,0 +1,52 @@ +id: rnaseq +title: RNASeq +tabs: + - id: overview + title: Overview + heading_md: + content: + - title_md: RNASeq workflow + description_md: | + RNA sequencing (RNASeq) measures gene expression levels across samples. + The workflow includes alignment, filtering, normalization, + differential expression analysis and visualization. + + - id: tools + title: Tools + content: + subsections: + + - id: alignment + title: Alignment + content: + - title_md: STAR - Align reads to reference + description_md: | + Align RNASeq reads to a reference genome using STAR. + button_md: Run STAR + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frgrnastar%2Frna_star" + + - id: analysis + title: Differential expression + content: + - title_md: edgeR + description_md: | + Differential gene expression analysis. + + - title_md: DESeq2 + description_md: | + Identify differentially expressed genes between groups. + + - id: visualisation + title: Visualisation + content: + - title_md: PCA + description_md: | + Explore sample clustering. + + - title_md: Heatmap + description_md: | + Display gene expression patterns. + + - title_md: Volcano plot + description_md: | + Visualise differential expression results. \ No newline at end of file From f4f03ed56b98f5079ec3b7fc060ef480fbc05380 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 11:47:12 -0400 Subject: [PATCH 12/51] Add RNASeq tools section with QC and alignment Added RNASeq tools including quality control (FastQC, MultiQC) and alignment (STAR). --- agrf/sections/rnaseq.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index f47b335..27c572d 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -15,7 +15,18 @@ tabs: title: Tools content: subsections: + + - id: qc + title: Quality control + content: + - title_md: FastQC + description_md: | + Assess raw RNASeq read quality including base quality scores, GC content and adapter contamination. + - title_md: MultiQC + description_md: | + Aggregate QC reports across multiple samples into a single summary report. + - id: alignment title: Alignment content: From 063ec75a727a5aa401d4f9081134ce5209046826 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 12:03:19 -0400 Subject: [PATCH 13/51] Add RNASeq gene quantification step (featureCounts) Added gene quantification step using featureCounts to convert aligned reads into count matrices for downstream differential expression analysis. --- agrf/sections/rnaseq.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 27c572d..39ec107 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -35,6 +35,24 @@ tabs: Align RNASeq reads to a reference genome using STAR. button_md: Run STAR button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frgrnastar%2Frna_star" + + - id: quantification + title: Gene quantification + content: + - title_md: featureCounts - Count reads per gene + description_md: | + Convert aligned reads (BAM files) into a gene count matrix required for downstream differential expression analysis. + + inputs: + - label: Aligned reads (BAM) + datatypes: + - bam + - label: Gene annotation file + datatypes: + - gtf + - gff + button_md: Run featureCounts + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts" - id: analysis title: Differential expression From 9f3c9d84687e5820d0c65343a630de0d090331e3 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 12:26:59 -0400 Subject: [PATCH 14/51] Add RNASeq filtering step Added filtering section including sample filtering and low count gene filtering to improve downstream differential expression analysis. --- agrf/sections/rnaseq.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 39ec107..34a53e0 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -54,6 +54,16 @@ tabs: button_md: Run featureCounts button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts" + - id: filtering + title: Filtering + content: + - title_md: Sample filtering + description_md: | + Remove outlier samples or unwanted groups before analysis. + - title_md: Filter lowly expressed genes + description_md: | + Remove genes with low counts across samples to improve statistical power in differential expression analysis. + - id: analysis title: Differential expression content: From 0673b174133b2c8e9b50605f3cfc97a7f16dabe2 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 12:42:39 -0400 Subject: [PATCH 15/51] Add normalization step to RNASeq workflow Added normalization section to explain adjustment of sequencing depth and library size. --- agrf/sections/rnaseq.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 34a53e0..a7b5ce4 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -63,6 +63,13 @@ tabs: - title_md: Filter lowly expressed genes description_md: | Remove genes with low counts across samples to improve statistical power in differential expression analysis. + + - id: normalization + title: Normalization + content: + - title_md: Normalization + description_md: | + Adjusts for differences in sequencing depth and library size between samples to allow accurate comparison of gene expression. - id: analysis title: Differential expression From 08e1600d9192c66e32cf69b2972138769bb5d2c8 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 13:00:46 -0400 Subject: [PATCH 16/51] correction very few corrections --- agrf/sections/rnaseq.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index a7b5ce4..e154882 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -60,7 +60,7 @@ tabs: - title_md: Sample filtering description_md: | Remove outlier samples or unwanted groups before analysis. - - title_md: Filter lowly expressed genes + - title_md: Filter lowly expressed genes description_md: | Remove genes with low counts across samples to improve statistical power in differential expression analysis. @@ -91,8 +91,8 @@ tabs: - title_md: Heatmap description_md: | - Display gene expression patterns. + Display gene expression patterns across samples. - title_md: Volcano plot description_md: | - Visualise differential expression results. \ No newline at end of file + Visualise differential expression results (log fold change vs significance). \ No newline at end of file From ba2a861cdf430b61d829a0ff934caf6502ce177f Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 14:17:01 -0400 Subject: [PATCH 17/51] Add input details for STAR alignment tool Added input file details (FASTQ, FASTA, GTF) for STAR alignment step in RNASeq workflow. --- agrf/sections/rnaseq.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index e154882..46c103a 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -33,6 +33,17 @@ tabs: - title_md: STAR - Align reads to reference description_md: | Align RNASeq reads to a reference genome using STAR. + + inputs: + - label: RNASeq reads (FASTQ) + datatypes: + - fastq + - label: Reference genome (fasta) + datatypes: + - fasta + - label: Gene annotation file (GTF) + datatypes: + - gtf button_md: Run STAR button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frgrnastar%2Frna_star" From 7fdeaa652137714ae257cb422c0b60175781879a Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 14:25:50 -0400 Subject: [PATCH 18/51] Add edgeR and DESeq2 inputs Added required inputs for differential expression analysis tools. --- agrf/sections/rnaseq.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 46c103a..30dc5e0 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -88,10 +88,24 @@ tabs: - title_md: edgeR description_md: | Differential gene expression analysis. + inputs: + - label: Gene count matrix + datatypes: + - tsv + - label: Sample metadata + datatypes: + - tsv - title_md: DESeq2 description_md: | Identify differentially expressed genes between groups. + inputs: + - label: Gene count matrix + datatypes: + - tsv + - label: Sample metadata + datatypes: + - tsv - id: visualisation title: Visualisation From 15819b2c92c9c63f74e23dedbf87ee6f391c72a9 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 19 Mar 2026 14:51:37 -0400 Subject: [PATCH 19/51] Add Metagenomics section to lab Created metagenomics.yml and added initial assembly tools (MEGAHIT, metaSPAdes/meta-hifiasm). Linked section in base.yml and homepage. --- agrf/sections/metagenomics.yml | 27 +++++++++++++++++++++++++++ agrf/static/local/base.yml | 1 + agrf/templates/intro.md | 3 +++ 3 files changed, 31 insertions(+) create mode 100644 agrf/sections/metagenomics.yml diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml new file mode 100644 index 0000000..fa998b4 --- /dev/null +++ b/agrf/sections/metagenomics.yml @@ -0,0 +1,27 @@ +id: metagenomics +title: Metagenomics + +tabs: + - id: overview + title: Overview + content: + - title_md: Metagenomics workflow + description_md: | + Metagenomics analysis involves assembly, binning, taxonomic classification, + and functional annotation of microbial communities. + + - id: tools + title: Tools + content: + subsections: + + - id: assembly + title: Assembly + content: + - title_md: MEGAHIT + description_md: | + Assemble short reads into contigs for metagenomic analysis. + + - title_md: metaSPAdes / meta-hifiasm + description_md: | + Assemble long-read or hybrid metagenomic data. \ No newline at end of file diff --git a/agrf/static/local/base.yml b/agrf/static/local/base.yml index 0ba1fbf..1bf6fe1 100644 --- a/agrf/static/local/base.yml +++ b/agrf/static/local/base.yml @@ -27,6 +27,7 @@ sections: - sections/qualitycontrol.yml - sections/microbial.yml - sections/rnaseq.yml + - sections/metagenomics.yml # - sections/moreanalysis.yml - sections/learn.yml # - sections/help.yml diff --git a/agrf/templates/intro.md b/agrf/templates/intro.md index 85dcf19..60ed3b8 100644 --- a/agrf/templates/intro.md +++ b/agrf/templates/intro.md @@ -79,6 +79,9 @@ then add Section, so data becomes dataSection
Galaxy Help
+
+
Metagenomics
+
Contact AGRF
From 725a72648f434dbaf46c769d860a4dda95561af5 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 20 Mar 2026 11:24:24 -0400 Subject: [PATCH 20/51] Add assembly + QC Added metagenomics workflow including assembly and assembly QC. --- agrf/sections/metagenomics.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index fa998b4..ffb830a 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -24,4 +24,11 @@ tabs: - title_md: metaSPAdes / meta-hifiasm description_md: | - Assemble long-read or hybrid metagenomic data. \ No newline at end of file + Assemble long-read or hybrid metagenomic data. + - id: assembly_qc + title: Assembly quality control + content: + - title_md: QUAST + description_md: | + Assess the quality of assembled contigs, including length, completeness and fragmentation. + From 5d400483478cd9ba949b0ea93ce8bcfa4910f9fc Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 20 Mar 2026 11:56:45 -0400 Subject: [PATCH 21/51] Add binning to metagenomics workflow Added MetaBAT binning with inputs. --- agrf/sections/metagenomics.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index ffb830a..c873ae6 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -31,4 +31,17 @@ tabs: - title_md: QUAST description_md: | Assess the quality of assembled contigs, including length, completeness and fragmentation. + - id: binning + title: Binning + content: + - title_md: MetaBAT2 + description_md: | + Group assembled contigs into genome bins representing individual microbial genomes. + inputs: + - label: Assembled contigs (FASTA) + datatypes: + - fasta + - label: BAM files (mapped reads) + datatypes: + - bam From 343fb9318bf204d1b4759366dd2905747d867d6a Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 20 Mar 2026 12:55:56 -0400 Subject: [PATCH 22/51] Add binning to metagenomics workflow Added MetaBAT for binning contigs into genome bins based on coverage and composition. --- agrf/sections/metagenomics.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index c873ae6..c2fdcdb 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -45,3 +45,14 @@ tabs: datatypes: - bam + - id: binning_qc + title: Binning quality control + content: + - title_md: CheckM2 + description_md: | + Assess genome bin quality by estimating completeness and contamination. + + inputs: + - label: Genome bins + datatypes: + - fasta \ No newline at end of file From 90882eff22d6db33c848b30d1e09d0989c9ff53f Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 20 Mar 2026 13:02:40 -0400 Subject: [PATCH 23/51] Add taxonomic classification to metagenomics workflow Added GTDB-Tk for assigning taxonomy to genome bins. --- agrf/sections/metagenomics.yml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index c2fdcdb..2ee215b 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -55,4 +55,15 @@ tabs: inputs: - label: Genome bins datatypes: - - fasta \ No newline at end of file + - fasta + + - id: taxonomy + title: Taxonomic classification + content: + - title_md: GTDB-Tk + description_md: | + Assign taxonomy to genome bins using the Genome Taxonomy Database. + inputs: + - label: Genome bins + datatypes: + - fasta \ No newline at end of file From 829ebc9ac4f9a085eeabbfd73e1adf7ba880645b Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 20 Mar 2026 14:37:51 -0400 Subject: [PATCH 24/51] Complete metagenomics workflow with inputs, outputs and tool links Added assembly, QC, binning, binning QC, and taxonomy steps with inputs, outputs, and Galaxy tool links. --- agrf/sections/metagenomics.yml | 40 +++++++++++++++++++++++++++++----- 1 file changed, 35 insertions(+), 5 deletions(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index 2ee215b..5f46801 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -21,6 +21,14 @@ tabs: - title_md: MEGAHIT description_md: | Assemble short reads into contigs for metagenomic analysis. + inputs: + - label: Sequencing reads (FASTQ) + datatypes: + - fastq + outputs: + - label: Assembled contigs (FASTA) + button_md: Run MEGAHIT + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit%2Fmegahit" - title_md: metaSPAdes / meta-hifiasm description_md: | @@ -31,6 +39,15 @@ tabs: - title_md: QUAST description_md: | Assess the quality of assembled contigs, including length, completeness and fragmentation. + inputs: + - label: Assembled contigs (FASTA) + datatypes: + - fasta + outputs: + - label: Assembly quality report + button_md: Run QUAST + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fquast%2Fquast" + - id: binning title: Binning content: @@ -44,6 +61,10 @@ tabs: - label: BAM files (mapped reads) datatypes: - bam + outputs: + - label: Genome bins (FASTA) + button_md: Run MetaBAT2 + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetabat2%2Fmetabat2" - id: binning_qc title: Binning quality control @@ -52,10 +73,15 @@ tabs: description_md: | Assess genome bin quality by estimating completeness and contamination. - inputs: - - label: Genome bins - datatypes: - - fasta + inputs: + - label: Genome bins (FASTA) + datatypes: + - fasta + outputs: + - label: Completeness and contamination report + button_md: Run CheckM2 + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcheckm2%2Fcheckm2" + - id: taxonomy title: Taxonomic classification @@ -66,4 +92,8 @@ tabs: inputs: - label: Genome bins datatypes: - - fasta \ No newline at end of file + - fasta + outputs: + - label: Taxonomic classification (TSV) + button_md: Run GTDB-Tk + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgtdbtk_classify_wf%2Fgtdbtk_classify_wf" \ No newline at end of file From 74f0c0f466b1690a9e930beb9b6feb4f007560b4 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 26 Mar 2026 11:31:33 -0400 Subject: [PATCH 25/51] Updated RNA-seq section with tool links and inputs. Added Galaxy tool links (FastQC, MultiQC, STAR, featureCounts, edgeR, DESeq2) and defined inputs for core analysis steps. --- agrf/old_base.yml | 0 agrf/sections/rnaseq.yml | 25 +++++++++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 agrf/old_base.yml diff --git a/agrf/old_base.yml b/agrf/old_base.yml new file mode 100644 index 0000000..e69de29 diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 30dc5e0..cf0c762 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -22,10 +22,25 @@ tabs: - title_md: FastQC description_md: | Assess raw RNASeq read quality including base quality scores, GC content and adapter contamination. + inputs: + - label: Sequencing reads (FASTQ) + datatypes: + - fastq + button_md: Run FastQC + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc" - title_md: MultiQC description_md: | Aggregate QC reports across multiple samples into a single summary report. + inputs: + - label: FastQC reports + datatypes: + - html + - zip + outputs: + - label: Summary QC report (HTML) + button_md: Run MultiQC + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmultiqc%2Fmultiqc" - id: alignment title: Alignment @@ -44,6 +59,8 @@ tabs: - label: Gene annotation file (GTF) datatypes: - gtf + outputs: + - label: Aligned reads (BAM) button_md: Run STAR button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frgrnastar%2Frna_star" @@ -62,6 +79,8 @@ tabs: datatypes: - gtf - gff + outputs: + - label: Gene count matrix (TSV) button_md: Run featureCounts button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts" @@ -95,6 +114,10 @@ tabs: - label: Sample metadata datatypes: - tsv + outputs: + - label: Differential expression results (TSV) + button_md: Run edgeR + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fedger%2Fedger" - title_md: DESeq2 description_md: | @@ -106,6 +129,8 @@ tabs: - label: Sample metadata datatypes: - tsv + button_md: Run DESeq2 + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdeseq2%2Fdeseq2" - id: visualisation title: Visualisation From 135b3eedd754b8a632468cb80e2b0b09bd5bb192 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 26 Mar 2026 12:28:39 -0400 Subject: [PATCH 26/51] Refined RNA-seq workflow and fixed visualization section. Updated RNA-seq workflow by removing PCA tool link and refining visualization steps. Ensured correct inputs, outputs, and tool links for all sections. --- agrf/sections/rnaseq.yml | 20 +++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index cf0c762..a0911e2 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -129,6 +129,8 @@ tabs: - label: Sample metadata datatypes: - tsv + outputs: + - label: Differential expression results (TSV) button_md: Run DESeq2 button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdeseq2%2Fdeseq2" @@ -137,12 +139,24 @@ tabs: content: - title_md: PCA description_md: | - Explore sample clustering. - + Explore sample clustering using principal component analysis. + - title_md: Heatmap description_md: | Display gene expression patterns across samples. + inputs: + - label: Expression matrix + datatypes: + - tsv + button_md: Run Heatmap + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_heatmap2%2Fggplot2_heatmap2" - title_md: Volcano plot description_md: | - Visualise differential expression results (log fold change vs significance). \ No newline at end of file + Visualise differential expression results (log fold change vs significance). + inputs: + - label: Differential expression results (TSV) + datatypes: + - tsv + button_md: Run Volcano plot + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot" \ No newline at end of file From cd5700cd68e424f795a66609df5e88f899806360 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 26 Mar 2026 14:51:27 -0400 Subject: [PATCH 27/51] Refine metagenomics workflow and add inputs Updated metagenomics workflow by refining descriptions, adding inputs , and improving tool clarity. Ensured alignment with standard assembly, binning, QC, and taxonomy steps. --- agrf/sections/metagenomics.yml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index 5f46801..74e7826 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -7,8 +7,8 @@ tabs: content: - title_md: Metagenomics workflow description_md: | - Metagenomics analysis involves assembly, binning, taxonomic classification, - and functional annotation of microbial communities. + Metagenomics analysis involves assembly, binning, quality assessment, and taxonomic classification + of microbial communities. - id: tools title: Tools @@ -32,7 +32,12 @@ tabs: - title_md: metaSPAdes / meta-hifiasm description_md: | - Assemble long-read or hybrid metagenomic data. + Assemble long-read or hybrid metagenomic data (e.g., PacBio). + inputs: + - label: Long reads (FASTQ) + datatypes: + - fastq + - id: assembly_qc title: Assembly quality control content: From 1a7ef45e7e14f53843d296bf2bbbb7982d3863cd Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Thu, 26 Mar 2026 15:36:39 -0400 Subject: [PATCH 28/51] Refine microbial workflow and fix tool links Updated microbial profiling workflow by correcting tool links, fixing beta diversity steps, and improving overall structure and clarity. --- agrf/sections/microbial.yml | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index ae214be..48f79c4 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -231,7 +231,7 @@ tabs: - title_md: qiime2 diversity alpha-phylogenetic - Calculate alpha diversity (with a phylogenetic tree) description_md: | - Phylogenetic alpha diversity metrics are useful when evolutionary distinctivness is relevant to your hypothesis (e.g., comparing ecosystems or communities with potentially different evolutionary histories). A common example (included om AGRF's analysis) is: + Phylogenetic alpha diversity metrics are useful when evolutionary distinctivness is relevant to your hypothesis (e.g., comparing ecosystems or communities with potentially different evolutionary histories). A common example (included in AGRF's analysis) is: * Faith's Phylogenetic Distance @@ -243,8 +243,7 @@ tabs: - qza button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_phylogenetic%2Fqiime2__diversity__alpha_phylogenetic" - button_link: /request/vcs - + - title_md: qiime2 diversity alpha-correlation - Correlate alpha diversity with sample metadata description_md: | Determine whether numeric sample metadata columns are correlated with alpha diversity. @@ -327,7 +326,7 @@ tabs: datatypes: - qza - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha%2Fqiime2__diversity__alpha" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta%2Fqiime2__diversity__beta" - title_md: qiime2 diversity beta-phylogenetic - Calculate beta diversity (with a phylogenetic tree) @@ -343,9 +342,8 @@ tabs: datatypes: - qza - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_phylogenetic%2Fqiime2__diversity__alpha_phylogenetic" - button_link: /request/vcs - + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_phylogenetic%2Fqiime2__diversity__beta_phylogenetic" + - title_md: qiime2 diversity beta-correlation - Correlate beta diversity with sample metadata description_md: | Determine whether numeric sample metadata columns are correlated with beta diversity. @@ -359,7 +357,7 @@ tabs: - qza - tsv - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_correlation%2Fqiime2__diversity__alpha_correlation" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_correlation%2Fqiime2__diversity__beta_correlation" - title_md: qiime2 diversity beta-group-significance - Correlate beta diversity with groups in sample metadata description_md: | @@ -374,7 +372,7 @@ tabs: - qza - tsv - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_group_significance%2Fqiime2__diversity__alpha_group_significance" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_group_significance%2Fqiime2__diversity__beta_group_significance" - title_md: qiime2 diversity pcoa - Principal coordinates analysis description_md: | @@ -399,7 +397,7 @@ tabs: datatypes: - qza - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_rarefaction%2Fqiime2__diversity__alpha_rarefaction" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_rarefaction%2Fqiime2__diversity__beta_rarefaction" - title_md: PICRUSt2 metagenome prediction - Predict microbial functions From 0501ddf81c04d1b3a569d1b52c287402e613ccba Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Mar 2026 11:24:30 -0400 Subject: [PATCH 29/51] Add microbial workflow with diversity analysis and tools 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. --- agrf/sections/microbial.yml | 90 +++++++++++++++++++++---------------- 1 file changed, 51 insertions(+), 39 deletions(-) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 48f79c4..9989bf5 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -96,9 +96,9 @@ tabs: title: Tools content: subsections: - - id: QIIME2_formats - title: Working with QIIME 2 files - content: + - id: QIIME2_formats + title: Working with QIIME 2 files + content: - title_md: Details description_md: | @@ -132,7 +132,6 @@ tabs: button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2_core__tools__export%2Fqiime2_core__tools__export" - - title_md: qiime2 feature-table summarize - Summarize feature table description_md: | Generate a summary of a feature table, including counts per sample and feature frequency distribution. @@ -166,8 +165,8 @@ tabs: - title_md: qiime2 feature-table filter-samples - Filter samples using metadata description_md: | - Remove samples from a feature table based on sample metadata. - This can be used to exclude groups or remove outlier samples before downstream analysis. + Filter samples using metadata to remove outliers or exclude specific groups before analysis. + inputs: - label: QIIME 2 Artifact file - FeatureTable[Frequency] datatypes: @@ -177,14 +176,14 @@ tabs: - tsv button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__filter_samples%2Fqiime2__feature_table__filter_samples" - - id: alpha_diversity - title: Alpha Diversity + - id: alpha_diversity + title: Alpha Diversity - content: + content: - - title_md: Details - description_md: | - Alpha diversity measures the diversity *within* a single sample. There are a number of different metrics used. AGRF's analysis includes four alpha diversity metrics (stored within separate .qza files). + - title_md: Details + description_md: | + Alpha diversity measures the diversity *within* a single sample. There are a number of different metrics used. AGRF's analysis includes four alpha diversity metrics (stored within separate .qza files). - `observed_features_vector.qza` - Sample richness per sample. A count of the number of features (i.e. species) observed per sample. - `shannon_vector.qza` - Shannon entropy (i.e. Shannon index) for each sample. This is a quantitative measure of community richness (number of species present) and evenness. Specifically, it quantifies the uncertainty in predicting the species of an individual microbe (or effectively a read) taken at random from the sample. @@ -194,14 +193,14 @@ tabs: Each .qza file contains alpha-diversity.tsv which can be extracted in Galaxy using the `qiime tools export` tool. The .tsv contains two columns: [sample name.fastq] , [alpha diversity metric] - inputs: + inputs: - label: QIIME 2 Artifact file - FeatureTable[Frequency] datatypes: - qza - - title_md: qiime2 diversity alpha - Calculate alpha diversity (non-phylogenetic) - description_md: | + - title_md: qiime2 diversity alpha - Calculate alpha diversity (non-phylogenetic) + description_md: | Non-phylogenetic alpha diversity metrics provide a general overview of diversity based on counts or proportions. Common examples (included in AGRF's analysis) are: * Observed features (richness) @@ -210,12 +209,12 @@ tabs: Use this tool to calculate other non-phylogenetic alpha diversity metrics. - inputs: + inputs: - label: QIIME 2 Artifact file - FeatureTable[Frequency] datatypes: - qza - buttons: + buttons: - icon: run link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha%2Fqiime2__diversity__alpha" tip: QIIME2 - Alpha diversity @@ -226,29 +225,29 @@ tabs: link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_phylogenetic%2Fqiime2__diversity__alpha_phylogenetic" tip: QIIME2 - Alpha diversity (phlyogenetic) - #button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha%2Fqiime2__diversity__alpha" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha%2Fqiime2__diversity__alpha" - - title_md: qiime2 diversity alpha-phylogenetic - Calculate alpha diversity (with a phylogenetic tree) - description_md: | + - title_md: qiime2 diversity alpha-phylogenetic - Calculate alpha diversity (with a phylogenetic tree) + description_md: | Phylogenetic alpha diversity metrics are useful when evolutionary distinctivness is relevant to your hypothesis (e.g., comparing ecosystems or communities with potentially different evolutionary histories). A common example (included in AGRF's analysis) is: * Faith's Phylogenetic Distance Use this tool to calculate other phylogenetic alpha diversity metrics. - inputs: + inputs: - label: QIIME 2 Artifact file - FeatureTable[Frequency] datatypes: - qza - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_phylogenetic%2Fqiime2__diversity__alpha_phylogenetic" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_phylogenetic%2Fqiime2__diversity__alpha_phylogenetic" - - title_md: qiime2 diversity alpha-correlation - Correlate alpha diversity with sample metadata - description_md: | + - title_md: qiime2 diversity alpha-correlation - Correlate alpha diversity with sample metadata + description_md: | Determine whether numeric sample metadata columns are correlated with alpha diversity. - inputs: + inputs: - label: QIIME 2 Artifact file - Alpha Diversity datatypes: - qza @@ -257,13 +256,13 @@ tabs: - qza - tsv - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_correlation%2Fqiime2__diversity__alpha_correlation" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_correlation%2Fqiime2__diversity__alpha_correlation" - - title_md: qiime2 diversity alpha-group-significance - Correlate alpha diversity with groups in sample metadata - description_md: | + - title_md: qiime2 diversity alpha-group-significance - Correlate alpha diversity with groups in sample metadata + description_md: | Visually and statistically compare groups of alpha diversity values. - inputs: + inputs: - label: QIIME 2 Artifact file - Alpha Diversity datatypes: - qza @@ -272,26 +271,26 @@ tabs: - qza - tsv - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_group_significance%2Fqiime2__diversity__alpha_group_significance" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_group_significance%2Fqiime2__diversity__alpha_group_significance" - - title_md: qiime2 diversity alpha-rarefaction - Assess sequencing depth sufficiency - description_md: | + - title_md: qiime2 diversity alpha-rarefaction - Assess sequencing depth sufficiency + description_md: | QIIME 2 repeatedly subsamples (rarefies) each sample’s sequence data at different depths (e.g., 1000, 2000, 3000 reads, etc.). For each depth, it calculates an alpha diversity metric (e.g., Shannon index, Faith's PD). It does this multiple times per depth to account for random variation (controlled by the --p-iterations parameter). The result is a curve for each sample showing diversity vs. sampling effort. - inputs: + inputs: - label: QIIME 2 Artifact file - FeatureTable[Frequency] datatypes: - qza - button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_rarefaction%2Fqiime2__diversity__alpha_rarefaction" + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__alpha_rarefaction%2Fqiime2__diversity__alpha_rarefaction" - - id: beta_diversity - title: Beta Diversity + - id: beta_diversity + title: Beta Diversity - content: + content: - title_md: Details description_md: | @@ -302,7 +301,7 @@ tabs: - `evenness_vector.qza` - Pielous evenness index for each sample. A measure of how close in numbers (sequence counts) each species in a sample is. It is the ratio of the Shannon index to the maximum possible Shannon index if every species was equally likely. Value between 0 and 1. The closer to 1 the more even. - `faith_pd_vector.qza` - Faiths phylogenetic distance. A phylogenetically aware alpha diversity metric. Equal to the sum of all branch lengths of the phylogenetic tree that spans all members of the sample. The higher the number the greater the diversity. - Each .qza file contains alpha-diversity.tsv which can be extracted in Galaxy using the `qiime tools export' tool. The .tsv contains two columns: `[sample name.fastq]` , `[alpha diversity metric]` + Each .qza file contains alpha-diversity.tsv which can be extracted in Galaxy using the `qiime tools export` tool. The .tsv contains two columns: `[sample name.fastq]` , `[alpha diversity metric]` inputs: @@ -331,7 +330,7 @@ tabs: - title_md: qiime2 diversity beta-phylogenetic - Calculate beta diversity (with a phylogenetic tree) description_md: | - Phylogenetic beta diversity metrics are useful when evolutionary distinctivness is relevant to your hypothesis (e.g., comparing ecosystems or communities with potentially different evolutionary histories). A common example (included om AGRF's analysis) is: + Phylogenetic beta diversity metrics are useful when evolutionary distinctivness is relevant to your hypothesis (e.g., comparing ecosystems or communities with potentially different evolutionary histories). A common example (included in AGRF's analysis) is: * Faith's Phylogenetic Distance @@ -399,7 +398,20 @@ tabs: button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__diversity__beta_rarefaction%2Fqiime2__diversity__beta_rarefaction" + - title_md: qiime2 composition ancom - Differential abundance of taxa + description_md: | + Identify taxa that are differentially abundant between groups using ANCOM. + inputs: + - label: Feature Table + datatypes: + - qza + - label: sample metadata + datatypes: + - tsv + button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__composition__ancom%2Fqiime2__composition__ancom" + + - title_md: PICRUSt2 metagenome prediction - Predict microbial functions description_md: | Predict microbial functional profiles such as gene families and metabolic pathways from microbial community data. From ca4202940ac18d3c09a641dabd918291c3837fc7 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Mar 2026 12:33:53 -0400 Subject: [PATCH 30/51] added trim galore Removes adapters, low-quality base and produces clean FASTQ reads for alignment --- agrf/sections/rnaseq.yml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index a0911e2..3728968 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -41,7 +41,18 @@ tabs: - label: Summary QC report (HTML) button_md: Run MultiQC button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmultiqc%2Fmultiqc" - + + - title_md: Trim Galore - Trim adapters and low-quality bases + description_md: | + Remove adapter sequences and low-quality bases from RNASeq reads before alignment. + inputs: + - label: Sequencing reads (FASTQ) + datatypes: + - fastq + outputs: + - label: Trimmed reads (FASTQ) + button_md: Run Trim Galore + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrim_galore%2Ftrim_galore" - id: alignment title: Alignment content: From 2cff7ffb9e346f3e77b4d40e6313a1f24aeae61a Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Mar 2026 12:52:01 -0400 Subject: [PATCH 31/51] Added Sortmerna to remove rRNA reads. Filters out ribosomal RNA to retain clean reads for alignment. --- agrf/sections/rnaseq.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 3728968..057a2a3 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -53,6 +53,20 @@ tabs: - label: Trimmed reads (FASTQ) button_md: Run Trim Galore button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrim_galore%2Ftrim_galore" + + - title_md: sortmerna + description_md: | + Remove rRNA reads from RNASeq data. + inputs: + - label: Sequencing reads (FASTQ) + datatypes: + - fastq + outputs: + - label: Filtered reads (FASTQ) + button_md: Run sortmerna + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fsortmerna%2Fbg_sortmerna" + + - id: alignment title: Alignment content: From c792cceb1d5413209a8b7fac696a8a2d8cdaf61d Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Mar 2026 13:06:03 -0400 Subject: [PATCH 32/51] Added Samtools Sort Sorts BAM files, organizes aligned reads by genomic position for downstream analysis. --- agrf/sections/rnaseq.yml | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 057a2a3..1b20c1e 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -66,7 +66,7 @@ tabs: button_md: Run sortmerna button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fsortmerna%2Fbg_sortmerna" - + - id: alignment title: Alignment content: @@ -88,6 +88,22 @@ tabs: - label: Aligned reads (BAM) button_md: Run STAR button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frgrnastar%2Frna_star" + + - id: post_alignment + title: BAM processing + content: + - title_md: samtools sort + description_md: | + Sort aligned reads (BAM) by genomic coordinates. + + inputs: + - label: Aligned reads (BAM) + datatypes: + - bam + outputs: + - label: Sorted BAM + button_md: Run samtools sort + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_sort%2Fsamtools_sort" - id: quantification title: Gene quantification From 2ddb08768fb7445c31bc8b90d11adf3247572702 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Mar 2026 13:10:11 -0400 Subject: [PATCH 33/51] Added StringTie Assembles transcripts from RNA-seq data, estimates gene expression from aligned reads. --- agrf/sections/rnaseq.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 1b20c1e..3110588 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -125,6 +125,21 @@ tabs: button_md: Run featureCounts button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts" + - title_md: StringTie + description_md: | + Assemble transcripts and estimate gene expression from aligned RNASeq reads. + inputs: + - label: Aligned reads (BAM) + datatypes: + - bam + - label: Reference annotation (GTF) + datatypes: + - gtf + outputs: + - label: Transcript assembly (GTF) + button_md: Run StringTie + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstringtie%2Fstringtie" + - id: filtering title: Filtering content: From 328692b7377fcbc64e71f0b27317f2f6c072ee2d Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Mar 2026 15:33:44 -0400 Subject: [PATCH 34/51] GBS analysis using ustacks, cstacks, sstacks, tsv2bam, gstacks, and populations. This workflow processes sequencing data to build loci, create a catalog, match samples, convert data, call SNPs, and generate population statistics. --- agrf/sections/moreanalysis.yml | 40 ++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/agrf/sections/moreanalysis.yml b/agrf/sections/moreanalysis.yml index c3925e3..32de14d 100644 --- a/agrf/sections/moreanalysis.yml +++ b/agrf/sections/moreanalysis.yml @@ -56,3 +56,43 @@ tabs: description_md: This tool does xyz - title_md: WF1 description_md: This wf does xyz + + - id: gbs + title: GBS + heading_md: > + content: + - title_md: ustacks + description_md: > + Build loci for each sample from sequencing reads. + button_md: Run ustacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_ustacks%2Fstacks_ustacks" + + - title_md: cstacks + description_md: > + Create a catalog of loci from multiple samples. + button_md: Run cstacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_cstacks%2Fstacks_cstacks" + . + - title_md: sstacks + description_md: > + Match individual samples to the catalog of loci. + button_md: Run sstacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_sstacks%2Fstacks2_sstacks" + + - title_md: tsv2bam + description_md: > + Convert stacks output into BAM format for downstream analysis. + button_md: Run tsv2bam + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_tsv2bam%2Fstacks2_tsv2bam" + + - title_md: gstacks + description_md: > + Assemble loci and call SNPs across all samples. + button_md: Run gstacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_gstacks%2Fstacks2_gstacks" + + - title_md: populations + description_md: > + Calculate population-level statistics and export variant data. + button_md: Run populations + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_populations%2Fstacks2_populations" \ No newline at end of file From 8d53eb11f09611ef2691735861f8289464e380fb Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 27 Mar 2026 15:58:00 -0400 Subject: [PATCH 35/51] Added tutorial section for RNASeq with transcriptomics GTN link. 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. --- agrf/sections/metagenomics.yml | 10 +++++++++- agrf/sections/rnaseq.yml | 12 +++++++++++- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index 74e7826..31e75e5 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -101,4 +101,12 @@ tabs: outputs: - label: Taxonomic classification (TSV) button_md: Run GTDB-Tk - button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgtdbtk_classify_wf%2Fgtdbtk_classify_wf" \ No newline at end of file + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgtdbtk_classify_wf%2Fgtdbtk_classify_wf" + + - id: tutorials + title: Tutorials + content: + - title_md: Metagenomics analysis tutorials + description_md: Learn how to perform metagenomic classification, assembly, and functional analysis in Galaxy. + button_md: Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/metagenomics/ \ No newline at end of file diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 3110588..e579edf 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -215,4 +215,14 @@ tabs: datatypes: - tsv button_md: Run Volcano plot - button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot" \ No newline at end of file + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot" + + + - id: tutorials + title: Tutorials + heading_md: + content: + - title_md: RNA-seq analysis workflow tutorial + description_md: tool + button_md: Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/transcriptomics/ \ No newline at end of file From ba69e09dbc5aa3d10d6d55e24a8a8c6daa850f66 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 10 Apr 2026 12:44:54 -0400 Subject: [PATCH 36/51] Improved RNASeq tools section with inline descriptions 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 --- agrf/sections/rnaseq.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index e579edf..37a1035 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -19,7 +19,7 @@ tabs: - id: qc title: Quality control content: - - title_md: FastQC + - title_md: FastQC - Assess sequencing read quality description_md: | Assess raw RNASeq read quality including base quality scores, GC content and adapter contamination. inputs: @@ -29,7 +29,7 @@ tabs: button_md: Run FastQC button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc" - - title_md: MultiQC + - title_md: MultiQC - Aggregate QC reports description_md: | Aggregate QC reports across multiple samples into a single summary report. inputs: @@ -54,7 +54,7 @@ tabs: button_md: Run Trim Galore button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrim_galore%2Ftrim_galore" - - title_md: sortmerna + - title_md: sortmerna - Remove rRNA contamination description_md: | Remove rRNA reads from RNASeq data. inputs: @@ -70,7 +70,7 @@ tabs: - id: alignment title: Alignment content: - - title_md: STAR - Align reads to reference + - title_md: STAR - Align reads to reference genome description_md: | Align RNASeq reads to a reference genome using STAR. @@ -92,7 +92,7 @@ tabs: - id: post_alignment title: BAM processing content: - - title_md: samtools sort + - title_md: samtools sort - Sort BAM files description_md: | Sort aligned reads (BAM) by genomic coordinates. @@ -125,7 +125,7 @@ tabs: button_md: Run featureCounts button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts" - - title_md: StringTie + - title_md: StringTie - Assemble and quantify transcripts description_md: | Assemble transcripts and estimate gene expression from aligned RNASeq reads. inputs: @@ -160,7 +160,7 @@ tabs: - id: analysis title: Differential expression content: - - title_md: edgeR + - title_md: edgeR - Differential expression analysis description_md: | Differential gene expression analysis. inputs: @@ -175,7 +175,7 @@ tabs: button_md: Run edgeR button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fedger%2Fedger" - - title_md: DESeq2 + - title_md: DESeq2 - Differential gene expression analysis description_md: | Identify differentially expressed genes between groups. inputs: @@ -193,11 +193,11 @@ tabs: - id: visualisation title: Visualisation content: - - title_md: PCA + - title_md: PCA - Visualise sample clustering description_md: | Explore sample clustering using principal component analysis. - - title_md: Heatmap + - title_md: Heatmap - Visualise gene expression patterns description_md: | Display gene expression patterns across samples. inputs: @@ -207,7 +207,7 @@ tabs: button_md: Run Heatmap button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fggplot2_heatmap2%2Fggplot2_heatmap2" - - title_md: Volcano plot + - title_md: Volcano plot - Visualise differential expression results description_md: | Visualise differential expression results (log fold change vs significance). inputs: From c9d74819702518ec7c49b7019495c2a09ce7759f Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 10 Apr 2026 12:53:47 -0400 Subject: [PATCH 37/51] Improved Metagenomics tools section with inline description Added concise inline descriptions to metagenomics tools for better readability and consistency. --- agrf/sections/metagenomics.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index 31e75e5..3821e58 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -18,7 +18,7 @@ tabs: - id: assembly title: Assembly content: - - title_md: MEGAHIT + - title_md: MEGAHIT - Assemble short-reads into contigs description_md: | Assemble short reads into contigs for metagenomic analysis. inputs: @@ -30,7 +30,7 @@ tabs: button_md: Run MEGAHIT button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit%2Fmegahit" - - title_md: metaSPAdes / meta-hifiasm + - title_md: metaSPAdes / meta-hifiasm - Assemble long-reads or hybrid reads description_md: | Assemble long-read or hybrid metagenomic data (e.g., PacBio). inputs: @@ -41,7 +41,7 @@ tabs: - id: assembly_qc title: Assembly quality control content: - - title_md: QUAST + - title_md: QUAST - Assess assembly quality description_md: | Assess the quality of assembled contigs, including length, completeness and fragmentation. inputs: @@ -56,7 +56,7 @@ tabs: - id: binning title: Binning content: - - title_md: MetaBAT2 + - title_md: MetaBAT2 - Bin contigs into genomes description_md: | Group assembled contigs into genome bins representing individual microbial genomes. inputs: @@ -74,7 +74,7 @@ tabs: - id: binning_qc title: Binning quality control content: - - title_md: CheckM2 + - title_md: CheckM2 - Assess completeness and contamination description_md: | Assess genome bin quality by estimating completeness and contamination. @@ -91,7 +91,7 @@ tabs: - id: taxonomy title: Taxonomic classification content: - - title_md: GTDB-Tk + - title_md: GTDB-Tk - Assign taxonomy to genome bins description_md: | Assign taxonomy to genome bins using the Genome Taxonomy Database. inputs: From f60f61b004dc8a47a51c12f07ce3839ebc2acc4e Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 12:21:55 -0400 Subject: [PATCH 38/51] Add GBS section with STACKS workflow, inputs/outputs, and tutorials 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. --- agrf/sections/gbs.yml | 110 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 110 insertions(+) create mode 100644 agrf/sections/gbs.yml diff --git a/agrf/sections/gbs.yml b/agrf/sections/gbs.yml new file mode 100644 index 0000000..f1dd4a0 --- /dev/null +++ b/agrf/sections/gbs.yml @@ -0,0 +1,110 @@ +id: gbs +title: GBS + +tabs: + - id: overview + title: Overview + content: + - title_md: GBS (ddRADSeq) workflow + description_md: | + Genotyping-by-sequencing (GBS/ddRADSeq) analysis using the STACKS pipeline. + This workflow supports locus construction, catalog matching, variant calling, + and downstream population genetics analysis. + + - id: tools + title: Tools + content: + subsections: + - id: stacks + title: STACKS workflow + content: + + - title_md: ustacks - Build loci for each sample + description_md: | + Build loci from sequencing reads for each sample. + inputs: + - label: Sequencing reads (FASTQ) + datatypes: + - fastqsanger + - fasta + outputs: + - label: Sample loci + button_md: Run ustacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_ustacks%2Fstacks_ustacks" + + - title_md: cstacks - Create catalog of loci + description_md: | + Create a catalog of loci across multiple samples. + inputs: + - label: Loci from multiple samples + datatypes: + - tabular + outputs: + - label: Catalog of loci + button_md: Run cstacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_cstacks%2Fstacks_cstacks" + + - title_md: sstacks - Match samples to catalog + description_md: | + Match each sample to the catalog of loci. + inputs: + - label: Sample loci + datatypes: + - tabular + - label: Catalog of loci + datatypes: + - tabular + outputs: + - label: Matches to catalog + button_md: Run sstacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_sstacks%2Fstacks2_sstacks" + + - title_md: tsv2bam - Convert TSV to BAM + description_md: | + Convert TSV genotype data into BAM format for downstream analysis. + inputs: + - label: Loci and polymorphism + datatypes: + - tabular + - label: Catalog of loci + datatypes: + - tabular + - label: Matches to catalog + datatypes: + - tabular + outputs: + - label: BAM alignments + button_md: Run tsv2bam + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_tsv2bam%2Fstacks2_tsv2bam" + + - title_md: gstacks - Assemble loci and call variants + description_md: | + Assemble loci, align reads, and perform variant calling. + inputs: + - label: BAM alignments + datatypes: + - bam + outputs: + - label: Variant calls and assembled loci + button_md: Run gstacks + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_gstacks%2Fstacks2_gstacks" + + - title_md: populations - Population genetics analysis + description_md: | + Generate population-level statistics and export results for downstream analysis. + inputs: + - label: Variant calls / loci + datatypes: + - vcf + outputs: + - label: Population statistics and export files + button_md: Run populations + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_populations%2Fstacks2_populations" + + - id: tutorials + title: Tutorials + content: + - title_md: GBS analysis tutorials + description_md: Explore Galaxy Training Network tutorials for variant analysis workflows relevant to GBS and population genomics studies. + button_md: Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/variant-analysis/ From d7877adf26d385dbe19cd59fa0e0cc1f2af1418f Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 12:22:39 -0400 Subject: [PATCH 39/51] updated intro.md Added GBS section into intro --- agrf/templates/intro.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/agrf/templates/intro.md b/agrf/templates/intro.md index 60ed3b8..2d91132 100644 --- a/agrf/templates/intro.md +++ b/agrf/templates/intro.md @@ -82,6 +82,9 @@ then add Section, so data becomes dataSection
Metagenomics
+
+
GBS
+
Contact AGRF
From 5a37b9ab4e11ebcfc7e813460bbb2099acd4ba8a Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 12:49:51 -0400 Subject: [PATCH 40/51] Added Learn Galaxy section with training resources and tutorials 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. --- agrf/sections/learn.yml | 56 ++++++++++++++++++++++++++++++++++++----- 1 file changed, 50 insertions(+), 6 deletions(-) diff --git a/agrf/sections/learn.yml b/agrf/sections/learn.yml index e756b22..2fc2617 100644 --- a/agrf/sections/learn.yml +++ b/agrf/sections/learn.yml @@ -1,14 +1,58 @@ id: learn title: Learn Galaxy + tabs: - id: overview title: Overview - heading_md: + heading_md: + Learn how to use Galaxy through tutorials, workflows, and official documentation. content: - - title_md: abc + - title_md: Galaxy Training Resources + description_md: | + Learn how to use Galaxy through step-by-step tutorials from the Galaxy Training Network. + These resources cover a wide range of bioinformatics workflows including RNA-seq, + microbiome analysis, metagenomics, and variant analysis. + button_md: Browse Tutorials + button_link: https://training.galaxyproject.org/training-material/ + + - title_md: Variant Analysis Tutorials + description_md: | + Explore tutorials for SNP calling, variant analysis, and related workflows + relevant to GBS and population genomics studies. + button_md: View Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/variant-analysis/ + + - title_md: Microbiome Tutorials + description_md: | + Learn microbial community analysis workflows in Galaxy, including QIIME 2 based + approaches for diversity analysis and taxonomic profiling. + button_md: View Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/microbiome/ + + - title_md: RNA-seq Tutorials + description_md: | + Learn RNA-seq analysis workflows in Galaxy, including alignment, quantification, + and differential expression analysis. + button_md: View Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/transcriptomics/ + + - title_md: Metagenomics Tutorials description_md: | - * abc + Explore tutorials for metagenome assembly, classification, and downstream + analysis workflows in Galaxy. + button_md: View Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/metagenomics/ - - button_md: Upload data - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1" \ No newline at end of file + - title_md: GBS and Population Genomics Tutorials + description_md: | + Learn workflows relevant to Genotyping-by-Sequencing (GBS), including variant calling, + SNP analysis, and population genomics approaches in Galaxy. + button_md: View Tutorials + button_link: https://training.galaxyproject.org/training-material/topics/variant-analysis/ + + - title_md: Galaxy Help and Documentation + description_md: | + Access official Galaxy documentation, user guides, and help resources to understand + tools, workflows, and data management in Galaxy. + button_md: Open Documentation + button_link: https://galaxyproject.org/learn/ \ No newline at end of file From 2c90d2383571af0321dff8220e7319bea4b0b60c Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 13:04:45 -0400 Subject: [PATCH 41/51] Updated microbial tutorial descriptions Replaced placeholder text with a clear description of microbiome analysis workflows in Galaxy, including diversity analysis and taxonomy. --- agrf/sections/microbial.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index 9989bf5..fbd93c2 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -465,7 +465,7 @@ tabs: content: - title_md: Calculating α and β diversity from microbiome taxonomic data - description_md: tool + description_md: Learn how to analyse microbiome data in Galaxy, including calculating alpha and beta diversity, exploring taxonomic composition, and visualising microbial community differences. button_md: Tutorials button_link: https://training.galaxyproject.org/training-material//topics/microbiome/tutorials/diversity/tutorial.html From 0e46bdf6306212e1b866f5471fd73909a3b9850a Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 13:05:07 -0400 Subject: [PATCH 42/51] Updated RNA-seq tutorials description Replaced placeholder text with a brief description of RNA-seq workflows, including alignment and differential expression analysis. --- agrf/sections/rnaseq.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 37a1035..b3dc214 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -223,6 +223,6 @@ tabs: heading_md: content: - title_md: RNA-seq analysis workflow tutorial - description_md: tool + description_md: Learn how to perform RNA-seq analysis in Galaxy, including read preprocessing, alignment, transcript assembly, and differential gene expression analysis. button_md: Tutorials button_link: https://training.galaxyproject.org/training-material/topics/transcriptomics/ \ No newline at end of file From 7068b5ce76e79b6961c3aff48ec235efe6f0267a Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 13:05:57 -0400 Subject: [PATCH 43/51] Improved metagenomics tutorials description Updated the description to better explain metagenomics workflows such as classification, assembly, and analysis in Galaxy. --- agrf/sections/metagenomics.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index 3821e58..1e6062c 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -107,6 +107,6 @@ tabs: title: Tutorials content: - title_md: Metagenomics analysis tutorials - description_md: Learn how to perform metagenomic classification, assembly, and functional analysis in Galaxy. + description_md: Learn how to perform metagenomic analysis in Galaxy, including taxonomic classification, assembly, binning, and downstream functional analysis workflows. button_md: Tutorials button_link: https://training.galaxyproject.org/training-material/topics/metagenomics/ \ No newline at end of file From 6a8b86f71691fe4a8737e945f42c85a77553dd36 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 13:41:22 -0400 Subject: [PATCH 44/51] Add Bakta to metagenomics tools Added Bakta for functional annotation of metagenomic assemblies. --- agrf/sections/metagenomics.yml | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index 1e6062c..0227c30 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -102,8 +102,23 @@ tabs: - label: Taxonomic classification (TSV) button_md: Run GTDB-Tk button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgtdbtk_classify_wf%2Fgtdbtk_classify_wf" - - - id: tutorials + + - id: functional_annotation + title: Functional annotation + content: + - title_md: Bakta - Functional annotation of genomes + description_md: | + Annotate assembled genomes and bins to identify genes and functional features. + This helps in understanding the biological roles of microbial communities. + inputs: + - label: Genome bins or contigs (FASTA) + datatypes: + - fasta + outputs: + - label: Annotated genomes and functional features + button_md: Run Bakta + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbakta%2Fbakta%2F1.9.4%2Bgalaxy1&version=latest" + - id: tutorials title: Tutorials content: - title_md: Metagenomics analysis tutorials From acc95debab13448cc1ee6578eeedbecb23ddedfc Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 15:45:09 -0400 Subject: [PATCH 45/51] Add MAFFT, BLAST, and FastTree tools to microbial section 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. --- agrf/sections/microbial.yml | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/agrf/sections/microbial.yml b/agrf/sections/microbial.yml index fbd93c2..aecbbb5 100644 --- a/agrf/sections/microbial.yml +++ b/agrf/sections/microbial.yml @@ -440,8 +440,6 @@ tabs: - qza button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__feature_table__heatmap%2Fqiime2__feature_table__heatmap" - - - title_md: qiime2 taxa barplot - Visualise taxonomic composition description_md: | Generate interactive stacked bar plots showing the relative abundance of taxa across samples. @@ -457,7 +455,26 @@ tabs: - tsv button_link: "{{ galaxy_base_url }}?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fq2d2%2Fqiime2__taxa__barplot%2Fqiime2__taxa__barplot" + - id: species_identification + title: Species identification and validation + content: + - title_md: BLAST - Identify sequences using database search + description_md: | + Compare sequences against reference databases to identify closest matching species. + button_md: Run BLAST + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_consensus_blast/qiime2__feature_classifier__classify_consensus_blast" + - title_md: MAFFT - Multiple sequence alignment + description_md: | + Align sequences with references for phylogenetic analysis. + button_md: Run MAFFT + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__alignment__mafft/qiime2__alignment__mafft" + + - title_md: FastTree - Build phylogenetic tree + description_md: | + Construct phylogenetic trees to compare samples with known species. + button_md: Run FastTree + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree" - id: tutorials title: Tutorials From c3d7f8a9bec3fa9b3710e7ee41c73acbaa01a863 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 17 Apr 2026 16:19:42 -0400 Subject: [PATCH 46/51] updated base.yml added gbs into base.yml --- agrf/static/local/base.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/agrf/static/local/base.yml b/agrf/static/local/base.yml index 1bf6fe1..5f2673f 100644 --- a/agrf/static/local/base.yml +++ b/agrf/static/local/base.yml @@ -28,6 +28,7 @@ sections: - sections/microbial.yml - sections/rnaseq.yml - sections/metagenomics.yml + - sections/gbs.yml # - sections/moreanalysis.yml - sections/learn.yml # - sections/help.yml From 4d3cd2ea0f00c7af0df570f67ef7c5695c44f2c1 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 24 Apr 2026 10:30:08 -0400 Subject: [PATCH 47/51] Add RNASeq overview, outputs, and file descriptions 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. --- agrf/sections/rnaseq.yml | 73 +++++++++++++++++++++++++++++++++++++--- 1 file changed, 68 insertions(+), 5 deletions(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index b3dc214..4b3aea6 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -3,13 +3,74 @@ title: RNASeq tabs: - id: overview title: Overview - heading_md: content: - - title_md: RNASeq workflow + - title_md: About the service description_md: | - RNA sequencing (RNASeq) measures gene expression levels across samples. - The workflow includes alignment, filtering, normalization, - differential expression analysis and visualization. + RNA sequencing (RNASeq) is used to quantify gene expression and identify differentially expressed genes across biological conditions. In this workflow, raw sequencing reads are quality checked, filtered, and aligned to a reference genome using STAR. Gene-level quantification is performed using featureCounts or StringTie, followed by statistical analysis using edgeR or DESeq2. + + This pipeline enables identification of transcriptional changes, biological pathway alterations, and potential biomarkers associated with experimental conditions. + + - title_md: Results include + description_md: | + RNASeq analysis generates multiple output files at different stages of the workflow. + + **Processed read data** + - Quality filtered FASTQ files (optional after trimming) + + **Alignment outputs** + - BAM files containing aligned reads + - Sorted and indexed BAM files + + **Quantification outputs** + - Gene-level count matrix (tabular format) + - Transcript abundance estimates (StringTie output) + + **Differential expression results** + - Tables of differentially expressed genes (log fold change, p-values, adjusted p-values) + + **Visualisation outputs** + - PCA plots (sample clustering) + - Heatmaps (expression patterns) + - Volcano plots (significance vs fold change) + + - title_md: What files are included? + description_md: | + **Raw Data** + - Demultiplexed FASTQ files (per sample) containing sequencing reads + + **Quality Control** + - FastQC reports (HTML) providing per-sample quality metrics + - MultiQC summary report aggregating quality results across all samples + + **Alignment** + - BAM files containing reads mapped to the reference genome + + **Quantification** + - Gene count matrix (.tsv or .txt) containing gene-level expression values + - Transcript abundance files (StringTie output) + + **Differential Expression** + - DEG results table (.tsv) including log fold change, p-values, and adjusted p-values + + **Visualisation** + - PCA plots, heatmaps, and volcano plots for downstream interpretation + + - title_md: File formats used + description_md: | + **.fastq** + - Raw sequencing reads + + **.bam** + - Binary alignment file storing mapped reads + + **.tsv / .txt** + - Tabular files containing gene counts and statistical results + + **.html** + - Quality control reports (FastQC, MultiQC) + + **.csv** + - Processed results and downstream analysis tables (e.g., DEG results) - id: tools title: Tools @@ -26,6 +87,8 @@ tabs: - label: Sequencing reads (FASTQ) datatypes: - fastq + outputs: + - label: FastQC report (HTML) button_md: Run FastQC button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc" From d2370386ca6b71a714a1734191ab57d0d061b17f Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 24 Apr 2026 10:54:27 -0400 Subject: [PATCH 48/51] Add Metagenomics overview and structured output tables MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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. --- agrf/sections/metagenomics.yml | 65 ++++++++++++++++++++++++++++++++-- 1 file changed, 62 insertions(+), 3 deletions(-) diff --git a/agrf/sections/metagenomics.yml b/agrf/sections/metagenomics.yml index 0227c30..ceb2a04 100644 --- a/agrf/sections/metagenomics.yml +++ b/agrf/sections/metagenomics.yml @@ -5,10 +5,69 @@ tabs: - id: overview title: Overview content: - - title_md: Metagenomics workflow + - title_md: About the service description_md: | - Metagenomics analysis involves assembly, binning, quality assessment, and taxonomic classification - of microbial communities. + Metagenomics analysis enables the study of microbial communities directly from environmental or host-associated samples without the need for culturing. + This workflow processes sequencing reads through assembly, quality assessment, genome binning, and taxonomic and functional annotation. + + Short-read assemblies are generated using MEGAHIT, while long-read assemblies are performed using meta-hifiasm. + Assembly quality is evaluated using QUAST, and genome binning is carried out using MetaBAT to reconstruct individual microbial genomes. + + Bin quality is assessed using CheckM2, which estimates genome completeness and contamination. + Taxonomic classification is performed using GTDB-Tk, and functional annotation is conducted using Bakta to identify genes and biological functions. + + This pipeline provides insights into microbial diversity, genome composition, and functional potential of complex microbial communities. + + - title_md: Results include + description_md: | + Metagenomics analysis generates multiple output files across different stages of the workflow. + + **Processed read data** + - Quality filtered sequencing reads (FASTQ files) + + **Assembly outputs** + - Contigs or assembled genomes representing microbial sequences + + **Assembly quality assessment** + - QUAST reports summarising assembly statistics (e.g., N50, contig length, total assembly size) + + **Genome binning** + - Genome bins representing reconstructed microbial genomes + + **Binning quality assessment** + - CheckM2 reports indicating completeness and contamination levels of genome bins + + **Taxonomic classification** + - GTDB-Tk results assigning taxonomy to genome bins + + **Functional annotation** + - Bakta outputs including gene predictions and functional annotations + + **Summary outputs** + - Tables and reports for downstream analysis and interpretation + + - title_md: What files are included? + description_md: | + | **Filename** | **Description** | + |-------------|----------------| + | Demultiplexed *.FASTQ files (per sample) | Raw sequencing reads for each sample | + | contigs.fasta | Assembled contigs generated from sequencing reads | + | quast_report.html | Assembly quality report including N50, contig length, and summary statistics | + | bins/*.fa | Genome bins representing reconstructed microbial genomes | + | checkm2_results.tsv | Genome bin quality metrics (completeness and contamination) | + | gtdbtk_classification.tsv | Taxonomic classification of genome bins using GTDB-Tk | + | bakta_annotations.tsv | Functional annotations including gene predictions and protein functions | + | summary_tables.tsv | Summary tables for downstream analysis and interpretation | + + - title_md: File formats used + description_md: | + | **Type** | **Description** | + |---------|----------------| + | .fastq | Raw sequencing reads | + | .fasta / .fa | Assembled contigs or genome bins | + | .tsv | Tabular files containing QC metrics, taxonomy, and annotations | + | .html | Quality reports (e.g., QUAST) | + | .gff | Gene annotations and genomic features | - id: tools title: Tools From 2d05417e13f4cabebc0829fb661969cae27979e9 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 24 Apr 2026 11:20:29 -0400 Subject: [PATCH 49/51] Added GBS (ddRADSeq) overview section with workflow description and outputs 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. --- agrf/sections/gbs.yml | 48 +++++++++++++++++++++++++++++++++++++++---- 1 file changed, 44 insertions(+), 4 deletions(-) diff --git a/agrf/sections/gbs.yml b/agrf/sections/gbs.yml index f1dd4a0..36fbe8e 100644 --- a/agrf/sections/gbs.yml +++ b/agrf/sections/gbs.yml @@ -5,11 +5,51 @@ tabs: - id: overview title: Overview content: - - title_md: GBS (ddRADSeq) workflow + - title_md: About the service description_md: | - Genotyping-by-sequencing (GBS/ddRADSeq) analysis using the STACKS pipeline. - This workflow supports locus construction, catalog matching, variant calling, - and downstream population genetics analysis. + Genotyping-by-sequencing (GBS/ddRADSeq) is used to identify genetic variants across multiple samples for population genetics and related studies. + + AGRF currently runs GBS analysis using NGSEP because it is efficient for larger sample sets. However, NGSEP is not currently available in Galaxy. This Galaxy section therefore provides STACKS tools as an alternative option for users who want to reanalyse raw FASTQ data in Galaxy. + + Users may also import existing VCF outputs into Galaxy for downstream filtering and analysis using tools such as VCFtools and PLINK. + + - title_md: Results include + description_md: | + **Raw read data** - Demultiplexed sequencing reads in FASTQ format + + **Variant calls** - VCF files containing SNP and genotype information + + **Consensus sequences** - FASTA files containing consensus sequences + + **Filtered variant outputs** - VCF files filtered by missingness, minor allele frequency, or other criteria + + **PLINK outputs** - Files prepared for downstream population genetic analysis + + **Distance and visualisation outputs** - IBS distance matrix and heatmap-style outputs for sample comparison + + - title_md: What files are included? + description_md: | + | **Filename** | **Description** | + |-------------|----------------| + | Demultiplexed *.FASTQ files | Raw sequencing reads for each sample | + | variants.vcf | Variant calls containing SNP and genotype information | + | consensus_sequences.fasta | Consensus sequences generated from variant/locus analysis | + | filtered_high_level.vcf | VCF filtered using stricter missingness and MAF thresholds | + | filtered_low_level.vcf | VCF filtered using less stringent missingness and MAF thresholds | + | populations.plink.* | PLINK-format files generated from VCF data | + | ibs_distance_matrix.tsv | Identity-by-state distance matrix for sample comparison | + | heatmap_output.html / .png | Visualisation output showing sample relatedness or clustering | + + - title_md: File formats used + description_md: | + | **Type** | **Description** | + |---------|----------------| + | .fastq | Raw sequencing reads | + | .vcf | Variant call format containing SNP and genotype data | + | .fasta / .fa | Consensus sequences or assembled loci | + | .ped / .map | PLINK genotype input files | + | .tsv / .txt | Tabular outputs, filtering summaries, or distance matrices | + | .html / .png | Visualisation outputs such as heatmaps | - id: tools title: Tools From 3ec900a49a1adcae0cff9ab500fd4642894981d2 Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 24 Apr 2026 11:28:16 -0400 Subject: [PATCH 50/51] Refined RNA-seq overview formatting and 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. --- agrf/sections/rnaseq.yml | 77 ++++++++++++++-------------------------- 1 file changed, 27 insertions(+), 50 deletions(-) diff --git a/agrf/sections/rnaseq.yml b/agrf/sections/rnaseq.yml index 4b3aea6..9af839e 100644 --- a/agrf/sections/rnaseq.yml +++ b/agrf/sections/rnaseq.yml @@ -6,72 +6,49 @@ tabs: content: - title_md: About the service description_md: | - RNA sequencing (RNASeq) is used to quantify gene expression and identify differentially expressed genes across biological conditions. In this workflow, raw sequencing reads are quality checked, filtered, and aligned to a reference genome using STAR. Gene-level quantification is performed using featureCounts or StringTie, followed by statistical analysis using edgeR or DESeq2. + RNA sequencing (RNASeq) is used to quantify gene expression and identify differentially expressed genes across biological conditions. + + In this workflow, raw sequencing reads are quality checked, trimmed if required, and aligned to a reference genome using STAR. Gene-level quantification is performed using featureCounts or StringTie, followed by statistical analysis using edgeR or DESeq2. This pipeline enables identification of transcriptional changes, biological pathway alterations, and potential biomarkers associated with experimental conditions. - title_md: Results include description_md: | - RNASeq analysis generates multiple output files at different stages of the workflow. + **Raw read data** - Demultiplexed sequencing reads in FASTQ format - **Processed read data** - - Quality filtered FASTQ files (optional after trimming) + **Quality control outputs** - FastQC reports and MultiQC summary - **Alignment outputs** - - BAM files containing aligned reads - - Sorted and indexed BAM files + **Alignment outputs** - BAM files containing mapped reads - **Quantification outputs** - - Gene-level count matrix (tabular format) - - Transcript abundance estimates (StringTie output) + **Quantification outputs** - Gene count matrices and transcript abundance estimates - **Differential expression results** - - Tables of differentially expressed genes (log fold change, p-values, adjusted p-values) + **Differential expression results** - Tables of differentially expressed genes (log fold change, p-values, adjusted p-values) - **Visualisation outputs** - - PCA plots (sample clustering) - - Heatmaps (expression patterns) - - Volcano plots (significance vs fold change) + **Visualisation outputs** - PCA plots, heatmaps, and volcano plots - title_md: What files are included? description_md: | - **Raw Data** - - Demultiplexed FASTQ files (per sample) containing sequencing reads - - **Quality Control** - - FastQC reports (HTML) providing per-sample quality metrics - - MultiQC summary report aggregating quality results across all samples - - **Alignment** - - BAM files containing reads mapped to the reference genome - - **Quantification** - - Gene count matrix (.tsv or .txt) containing gene-level expression values - - Transcript abundance files (StringTie output) - - **Differential Expression** - - DEG results table (.tsv) including log fold change, p-values, and adjusted p-values - - **Visualisation** - - PCA plots, heatmaps, and volcano plots for downstream interpretation + | **Filename** | **Description** | + |-------------|----------------| + | Demultiplexed *.FASTQ files | Raw sequencing reads for each sample | + | fastqc_report.html / multiqc_report.html | Quality control reports | + | aligned_reads.bam | Reads aligned to the reference genome | + | gene_counts.tsv | Gene-level count matrix | + | transcript_abundance.tsv | Transcript abundance estimates (StringTie output) | + | deg_results.tsv | Differential expression results (logFC, p-values, adjusted p-values) | + | pca_plot.png | Sample clustering visualisation | + | heatmap.png | Expression pattern visualisation | + | volcano_plot.png | Significance vs fold-change visualisation | - title_md: File formats used description_md: | - **.fastq** - - Raw sequencing reads - - **.bam** - - Binary alignment file storing mapped reads - - **.tsv / .txt** - - Tabular files containing gene counts and statistical results - - **.html** - - Quality control reports (FastQC, MultiQC) - - **.csv** - - Processed results and downstream analysis tables (e.g., DEG results) - + | **Type** | **Description** | + |---------|----------------| + | .fastq | Raw sequencing reads | + | .bam | Binary alignment files storing mapped reads | + | .tsv / .txt | Tabular files containing counts and statistical results | + | .html | Quality control reports (FastQC, MultiQC) | + | .png | Visualisation outputs such as PCA, heatmaps, and volcano plots | - id: tools title: Tools content: From d7823970b5f769846f4a431f7d9bb518bbce43bd Mon Sep 17 00:00:00 2001 From: tojoa10 Date: Fri, 24 Apr 2026 12:25:04 -0400 Subject: [PATCH 51/51] Update GBS section with tools, outputs, and bcftools filtering 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. --- agrf/sections/gbs.yml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/agrf/sections/gbs.yml b/agrf/sections/gbs.yml index 36fbe8e..7cc8177 100644 --- a/agrf/sections/gbs.yml +++ b/agrf/sections/gbs.yml @@ -7,12 +7,11 @@ tabs: content: - title_md: About the service description_md: | - Genotyping-by-sequencing (GBS/ddRADSeq) is used to identify genetic variants across multiple samples for population genetics and related studies. + Genotyping-by-sequencing (GBS/ddRADSeq) is used to identify genetic variants across multiple samples for population genetics studies. - AGRF currently runs GBS analysis using NGSEP because it is efficient for larger sample sets. However, NGSEP is not currently available in Galaxy. This Galaxy section therefore provides STACKS tools as an alternative option for users who want to reanalyse raw FASTQ data in Galaxy. - - Users may also import existing VCF outputs into Galaxy for downstream filtering and analysis using tools such as VCFtools and PLINK. + AGRF performs primary GBS analysis using NGSEP due to its efficiency for large sample sets. The outputs typically include variant call files (VCF) and consensus sequences (FASTA). + This Galaxy section supports downstream analysis of these outputs. Users can import VCF files into Galaxy and perform variant filtering, population genetic analysis, and visualisation using tools such as VCFtools and PLINK. - title_md: Results include description_md: | **Raw read data** - Demultiplexed sequencing reads in FASTQ format @@ -66,7 +65,6 @@ tabs: - label: Sequencing reads (FASTQ) datatypes: - fastqsanger - - fasta outputs: - label: Sample loci button_md: Run ustacks @@ -141,6 +139,11 @@ tabs: button_md: Run populations button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_populations%2Fstacks2_populations" + - title_md: bcftools filter - Filter variant data + description_md: Filter variant call files (VCF) based on minor allele frequency (MAF), missing data thresholds, and quality metrics for downstream population analysis. + button_md: Launch Tool + button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_filter%2Fbcftools_filter" + - id: tutorials title: Tutorials content: