diff --git a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml index f6cc84cd..9c4e7a06 100644 --- a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml +++ b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml @@ -5,34 +5,443 @@ tabs: title: Workflows heading_md: > - content: [] + content: + - title_md: AMR-Pathfinder + description_md: AMR-Pathfinder + button_link: https://workflowhub.eu/workflows/1189?version=2 + - title_md: bacterial-genome-assembly/main + description_md: bacterial-genome-assembly/main + button_link: https://workflowhub.eu/workflows/1043?version=7 + - title_md: quality-and-contamination-control/main + description_md: quality-and-contamination-control/main + button_link: https://workflowhub.eu/workflows/1052?version=8 + - title_md: 'Workflow 4: Staramr' + description_md: 'Workflow 4: Staramr' + button_link: https://workflowhub.eu/workflows/470?version=1 + - title_md: bacterial_genome_annotation/main + description_md: bacterial_genome_annotation/main + button_link: https://workflowhub.eu/workflows/1050?version=9 + - title_md: amr_gene_detection/main + description_md: amr_gene_detection/main + button_link: https://workflowhub.eu/workflows/1049?version=7 + - title_md: pox-virus-amplicon/main + description_md: pox-virus-amplicon/main + button_link: https://workflowhub.eu/workflows/439?version=2 + - title_md: '3: Plant virus exploration' + description_md: '3: Plant virus exploration' + button_link: https://workflowhub.eu/workflows/103?version=1 + - title_md: '2: Plant virus confirmation' + description_md: '2: Plant virus confirmation' + button_link: https://workflowhub.eu/workflows/102?version=1 + - title_md: '1: Plant virus detection with kraken2 (SE)' + description_md: '1: Plant virus detection with kraken2 (SE)' + button_link: https://workflowhub.eu/workflows/124?version=1 + - title_md: '1: Plant virus detection with kraken2 (PE)' + description_md: '1: Plant virus detection with kraken2 (PE)' + button_link: https://workflowhub.eu/workflows/101?version=1 + - title_md: Halophiles workup of Comparative gene analysis + description_md: Halophiles workup of Comparative gene analysis + button_link: https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 + - title_md: pAllori Blood RNA + description_md: pAllori Blood RNA + button_link: https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 + - title_md: Metaproteomics workflow + description_md: Metaproteomics workflow + button_link: https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 + - title_md: Feature-Count Table Normalization + description_md: Feature-Count Table Normalization + button_link: https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 + - title_md: metaQuantome_datacreation_workflow + description_md: metaQuantome_datacreation_workflow + button_link: https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 + - title_md: metaquantome-function-worklow + description_md: metaquantome-function-worklow + button_link: https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 + - title_md: Allele-based Pathogen Identification (release v0.1.2) + description_md: Allele-based Pathogen Identification (release v0.1.2) + button_link: https://usegalaxy.eu/published/workflow?id=64abcddeb516a712 + - title_md: Taxonomy Profiling and Visualization with Kron (release v0.1) + description_md: Taxonomy Profiling and Visualization with Kron (release v0.1) + button_link: https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 + - title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release + v0.1) + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + (release v0.1) + button_link: https://usegalaxy.eu/published/workflow?id=f6a763951d815944 + - title_md: Nanopore Preprocessing (release v0.1) + description_md: Nanopore Preprocessing (release v0.1) + button_link: https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 + - title_md: Gene-based Pathogen Identification (release v0.1) + description_md: Gene-based Pathogen Identification (release v0.1) + button_link: https://usegalaxy.eu/published/workflow?id=77e5bbd317750915 + - title_md: Allele-based Pathogen Identification (release v0.1) + description_md: Allele-based Pathogen Identification (release v0.1) + button_link: https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc + - title_md: Allele-based Pathogen Identification (release v0.1.1) + description_md: Allele-based Pathogen Identification (release v0.1.1) + button_link: https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f + - title_md: pAllori WGS + description_md: pAllori WGS + button_link: https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 + - title_md: MAGs workflow + description_md: MAGs workflow + button_link: https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 + - title_md: PathoGFAIR + description_md: PathoGFAIR + button_link: https://usegalaxy.eu/published/workflow?id=0dce37adb369492c + - title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + button_link: https://usegalaxy.eu/published/workflow?id=376119528377a3ae + - title_md: Allele-based Pathogen Identification + description_md: Allele-based Pathogen Identification + button_link: https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 + - title_md: Nanopore Preprocessing + description_md: Nanopore Preprocessing + button_link: https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c + - title_md: Taxonomy Profiling and Visualization with Phinch + description_md: Taxonomy Profiling and Visualization with Phinch + button_link: https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 + - title_md: metaQuantome_datacreation_workflow + description_md: metaQuantome_datacreation_workflow + button_link: https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d + - title_md: Gene-based Pathogen Identification + description_md: Gene-based Pathogen Identification + button_link: https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc + - title_md: Taxonomy Profiling and Visualization with Krona + description_md: Taxonomy Profiling and Visualization with Krona + button_link: https://usegalaxy.eu/published/workflow?id=10101558b211a782 + - title_md: Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool + description_md: Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool + button_link: https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 + - title_md: Mgnify ML + description_md: Mgnify ML + button_link: https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf + - title_md: Normalization + description_md: Normalization + button_link: https://usegalaxy.eu/published/workflow?id=0603f0898211f806 + - title_md: WF1_Database_Generation_Workflow + description_md: WF1_Database_Generation_Workflow + button_link: https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 + - title_md: WF2_Discovery-Workflow + description_md: WF2_Discovery-Workflow + button_link: https://usegalaxy.eu/published/workflow?id=8af41219411062ad + - title_md: WF3_VERIFICATION_WORKFLOW + description_md: WF3_VERIFICATION_WORKFLOW + button_link: https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d + - title_md: WF4_Quantitation_Workflow + description_md: WF4_Quantitation_Workflow + button_link: https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb + - title_md: WF5_Data_Interpretation_Worklow + description_md: WF5_Data_Interpretation_Worklow + button_link: https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 + - title_md: MetaG_extended + description_md: MetaG_extended + button_link: https://usegalaxy.eu/published/workflow?id=d57d41e306241396 + - title_md: MetaP + description_md: MetaP + button_link: https://usegalaxy.eu/published/workflow?id=01ac8bf9832789e2 + - title_md: MetaT + description_md: MetaT + button_link: https://usegalaxy.eu/published/workflow?id=3733bcdf5b458be7 + - title_md: metaquantome-taxonomy-workflow + description_md: metaquantome-taxonomy-workflow + button_link: https://usegalaxy.eu/published/workflow?id=695f7defb516d80d + - title_md: metaquantome-function-worklow + description_md: metaquantome-function-worklow + button_link: https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba + - title_md: Metaproteomics_GTN + description_md: Metaproteomics_GTN + button_link: https://usegalaxy.eu/published/workflow?id=68967c922de149ae + - title_md: Ecoli Comparison + description_md: Ecoli Comparison + button_link: https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 + - title_md: Main Metatranscriptomics Analysis + description_md: Main Metatranscriptomics Analysis + button_link: https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3 + - title_md: workflow-generate-dataset-for-assembly-tutorial + description_md: workflow-generate-dataset-for-assembly-tutorial + button_link: https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 + - title_md: Metagenomics assembly tutorial workflow + description_md: Metagenomics assembly tutorial workflow + button_link: https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 + - title_md: Microbial Variant Calling + description_md: Microbial Variant Calling + button_link: https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c + - title_md: Calling variants in non-diploid systems + description_md: Calling variants in non-diploid systems + button_link: https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb + - title_md: Comparative gene analysis + description_md: Comparative gene analysis + button_link: https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d + - title_md: Unicycler training + description_md: Unicycler training + button_link: https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 + - title_md: Apollo Load Test + description_md: Apollo Load Test + button_link: https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 + - title_md: Genome Annotation with Prokka [Feb 2020] + description_md: Genome Annotation with Prokka [Feb 2020] + button_link: https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 + - title_md: Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) + description_md: Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) + button_link: https://usegalaxy.eu/published/workflow?id=152223c8aed27357 + - title_md: Mtb phylogeny + description_md: Mtb phylogeny + button_link: https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 + - title_md: From VCFs to SNP distance matrix + description_md: From VCFs to SNP distance matrix + button_link: https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 + - title_md: From Fastqs to VCFs and BAMs + description_md: From Fastqs to VCFs and BAMs + button_link: https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 + - title_md: From BAMs to drug resistance prediction with TB-profiler + description_md: From BAMs to drug resistance prediction with TB-profiler + button_link: https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 + - title_md: M. tuberculosis Variant Analysis tutorial + description_md: M. tuberculosis Variant Analysis tutorial + button_link: https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b + - title_md: Compute Allel Frequency Table from paired reads + description_md: Compute Allel Frequency Table from paired reads + button_link: https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 + - title_md: Reference genome choice (indels, coverage, depth) for short reads + description_md: Reference genome choice (indels, coverage, depth) for short reads + button_link: https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 + - title_md: MGnify amplicon rRNA-prediction + ITS + description_md: MGnify amplicon rRNA-prediction + ITS + button_link: https://usegalaxy.eu/published/workflow?id=437704898229dfb6 + - title_md: MGnify amplicon QC + description_md: MGnify amplicon QC + button_link: https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 + - title_md: pAllori ASiam Functional Information MT + description_md: pAllori ASiam Functional Information MT + button_link: https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 + - title_md: ' pAllori ASiam Community Profile MT' + description_md: ' pAllori ASiam Community Profile MT' + button_link: https://usegalaxy.eu/published/workflow?id=05f5f040337786bf + - title_md: ' pAllori ASiam Preprocessing MT' + description_md: ' pAllori ASiam Preprocessing MT' + button_link: https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a + - title_md: MetaP + description_md: MetaP + button_link: https://usegalaxy.eu/published/workflow?id=96d198ed953449fd + - title_md: MetaG_extended + description_md: MetaG_extended + button_link: https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e + - title_md: MetaT + description_md: MetaT + button_link: https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b + - title_md: Allele-based Pathogen Identification (release v0.1.1) + description_md: Allele-based Pathogen Identification (release v0.1.1) + button_link: https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f + - title_md: Allele-based Pathogen Identification (release v0.1.2) + description_md: Allele-based Pathogen Identification (release v0.1.2) + button_link: https://usegalaxy.org/published/workflow?id=6d778eeb176d563c + - title_md: Taxonomy Profiling and Visualization with Kron (release v0.1) + description_md: Taxonomy Profiling and Visualization with Kron (release v0.1) + button_link: https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b + - title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release + v0.1) + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + (release v0.1) + button_link: https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc + - title_md: Gene-based Pathogen Identification (release v0.1) + description_md: Gene-based Pathogen Identification (release v0.1) + button_link: https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 + - title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + button_link: https://usegalaxy.org/published/workflow?id=2d3063882d8239ff + - title_md: PathoGFAIR (imported from uploaded file) + description_md: PathoGFAIR (imported from uploaded file) + button_link: https://usegalaxy.org/published/workflow?id=e55593af91337a05 + - title_md: Taxonomy Profiling and Visualization with Krona + description_md: Taxonomy Profiling and Visualization with Krona + button_link: https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4 + - title_md: Gene-based Pathogen Identification + description_md: Gene-based Pathogen Identification + button_link: https://usegalaxy.org/published/workflow?id=cce88bc57b180d09 + - title_md: Allele-based Pathogen Identification + description_md: Allele-based Pathogen Identification + button_link: https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6 + - title_md: Nanopore Preprocessing + description_md: Nanopore Preprocessing + button_link: https://usegalaxy.org/published/workflow?id=574e42683dc3961b + - title_md: Allele-based Pathogen Identification (release v0.1.2) + description_md: Allele-based Pathogen Identification (release v0.1.2) + button_link: https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba + - title_md: Taxonomy Profiling and Visualization with Kron (release v0.1) + description_md: Taxonomy Profiling and Visualization with Kron (release v0.1) + button_link: https://usegalaxy.org.au/published/workflow?id=131636a795bac485 + - title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release + v0.1) + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + (release v0.1) + button_link: https://usegalaxy.org.au/published/workflow?id=b60922a253df6654 + - title_md: Nanopore Preprocessing (release v0.1) + description_md: Nanopore Preprocessing (release v0.1) + button_link: https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2 + - title_md: Gene-based Pathogen Identification (release v0.1) + description_md: Gene-based Pathogen Identification (release v0.1) + button_link: https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060 + - title_md: PathoGFAIR (imported from uploaded file) + description_md: PathoGFAIR (imported from uploaded file) + button_link: https://usegalaxy.org.au/published/workflow?id=f5f9808fb50b6f2c + - title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + button_link: https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4 + - title_md: Allele-based Pathogen Identification + description_md: Allele-based Pathogen Identification + button_link: https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad + - title_md: Gene-based Pathogen Identification + description_md: Gene-based Pathogen Identification + button_link: https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2 + - title_md: Taxonomy Profiling and Visualization with Krona + description_md: Taxonomy Profiling and Visualization with Krona + button_link: https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417 + - title_md: Nanopore Preprocessing + description_md: Nanopore Preprocessing + button_link: https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b + - id: tutorials title: Tutorials - heading_md: > - - content: [] + heading_md: > - - id: pathways - title: Learning pathways - heading_md: > - Connected tutorials to train you to perform microbial data analysis fast!. content: - - title_md: Introduction to Galaxy and Sequence analysis - description_md: > - New to Galaxy and/or the field of genomics? In this learing pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. + - title_md: Making sense of a newly assembled genome + description_md: Making sense of a newly assembled genome button_link: - - title_md: Genome annotation for prokaryotes - description_md: > - + https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html + - title_md: Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina + MiSeq Data + description_md: Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina + MiSeq Data button_link: - - title_md: Detection of AMR genes in bacterial genomes - description_md: > - + https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html + - title_md: Assembly of metagenomic sequencing data + description_md: Assembly of metagenomic sequencing data button_link: - - - id: faq - title: FAQ - heading_md: > - - content: [] \ No newline at end of file + https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html + - title_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally + Illumina data) + description_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally + Illumina data) + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html + - title_md: Unicycler Assembly + description_md: Unicycler Assembly + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html + - title_md: Checking expected species and contamination in bacterial isolate + description_md: Checking expected species and contamination in bacterial isolate + button_link: + https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html + - title_md: Tree thinking for tuberculosis evolution and epidemiology + description_md: Tree thinking for tuberculosis evolution and epidemiology + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html + - title_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + description_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html + - title_md: Genome annotation with Prokka + description_md: Genome annotation with Prokka + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html + - title_md: Refining Genome Annotations with Apollo (prokaryotes) + description_md: Refining Genome Annotations with Apollo (prokaryotes) + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + - title_md: Identification of AMR genes in an assembled bacterial genome + description_md: Identification of AMR genes in an assembled bacterial genome + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html + - title_md: Bacterial Genome Annotation + description_md: Bacterial Genome Annotation + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html + - title_md: Comparative gene analysis in unannotated genomes + description_md: Comparative gene analysis in unannotated genomes + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html + - title_md: Essential genes detection with Transposon insertion sequencing + description_md: Essential genes detection with Transposon insertion sequencing + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html + - title_md: Genome annotation with Prokka + description_md: Genome annotation with Prokka + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html + - title_md: Making sense of a newly assembled genome + description_md: Making sense of a newly assembled genome + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html + - title_md: Microbial Variant Calling + description_md: Microbial Variant Calling + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html + - title_md: Refining Genome Annotations with Apollo (prokaryotes) + description_md: Refining Genome Annotations with Apollo (prokaryotes) + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + - title_md: Identification of AMR genes in an assembled bacterial genome + description_md: Identification of AMR genes in an assembled bacterial genome + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html + - title_md: Bacterial Genome Annotation + description_md: Bacterial Genome Annotation + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html + - title_md: Tree thinking for tuberculosis evolution and epidemiology + description_md: Tree thinking for tuberculosis evolution and epidemiology + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html + - title_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + description_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html + - title_md: M. tuberculosis Variant Analysis + description_md: M. tuberculosis Variant Analysis + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html + - title_md: Identification of AMR genes in an assembled bacterial genome + description_md: Identification of AMR genes in an assembled bacterial genome + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html + - title_md: 'metaQuantome 1: Data creation' + description_md: 'metaQuantome 1: Data creation' + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html + - title_md: Metaproteomics tutorial + description_md: Metaproteomics tutorial + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html + - title_md: 'metaQuantome 2: Function' + description_md: 'metaQuantome 2: Function' + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html + - title_md: 'metaQuantome 3: Taxonomy' + description_md: 'metaQuantome 3: Taxonomy' + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html + - title_md: Quality and contamination control in bacterial isolate using Illumina + MiSeq Data + description_md: Quality and contamination control in bacterial isolate using Illumina + MiSeq Data + button_link: + https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html + - title_md: Calling variants in non-diploid systems + description_md: Calling variants in non-diploid systems + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html + - title_md: M. tuberculosis Variant Analysis + description_md: M. tuberculosis Variant Analysis + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html + - title_md: Microbial Variant Calling + description_md: Microbial Variant Calling + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/3_microbiome.yml b/communities/microgalaxy/lab/sections/3_microbiome.yml index 5e339542..f5918772 100644 --- a/communities/microgalaxy/lab/sections/3_microbiome.yml +++ b/communities/microgalaxy/lab/sections/3_microbiome.yml @@ -5,34 +5,162 @@ tabs: title: Workflows heading_md: > - content: [] + content: + - title_md: Taxonomy classification using Kraken2 and Bracken + description_md: Taxonomy classification using Kraken2 and Bracken + button_link: https://workflowhub.eu/workflows/1199?version=2 + - title_md: Analyses of shotgun metagenomics data with MetaPhlAn2 + description_md: Analyses of shotgun metagenomics data with MetaPhlAn2 + button_link: https://workflowhub.eu/workflows/624?version=1 + - title_md: 'Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]' + button_link: https://workflowhub.eu/workflows/653?version=1 + - title_md: 'Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]' + button_link: https://workflowhub.eu/workflows/652?version=1 + - title_md: 'Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]' + button_link: https://workflowhub.eu/workflows/651?version=1 + - title_md: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With + Mothur]' + description_md: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis + With Mothur]' + button_link: https://workflowhub.eu/workflows/650?version=1 + - title_md: 'Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 1: Further Quality Control [16S Microbial Analysis With + Mothur]' + button_link: https://workflowhub.eu/workflows/648?version=1 + - title_md: 'Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis + With Mothur]' + description_md: 'Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis + With Mothur]' + button_link: https://workflowhub.eu/workflows/649?version=1 + - title_md: GTN Training - Antibiotic Resistance Detection + description_md: GTN Training - Antibiotic Resistance Detection + button_link: https://workflowhub.eu/workflows/406?version=1 + - title_md: pAllori Amplicon 16S Pre-Processing and Taxonomy Classification + description_md: pAllori Amplicon 16S Pre-Processing and Taxonomy Classification + button_link: https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 + - title_md: Cloud Aerosol MT-MG Contamination Filtering + description_md: Cloud Aerosol MT-MG Contamination Filtering + button_link: https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 + - title_md: Metatranscriptomics data analysis + description_md: Metatranscriptomics data analysis + button_link: https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 + - title_md: ' Cloud-Aerosole MT-MG Functional Profiling' + description_md: ' Cloud-Aerosole MT-MG Functional Profiling' + button_link: https://usegalaxy.eu/published/workflow?id=63478edcea3f449a + - title_md: Cloud-Aerosole MT-MG Pre-Processing + description_md: Cloud-Aerosole MT-MG Pre-Processing + button_link: https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 + - title_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + description_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + button_link: https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c + - title_md: Copy Of GTN Training - Antibiotic Resistance Detection + description_md: Copy Of GTN Training - Antibiotic Resistance Detection + button_link: https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa + - title_md: Identification of the micro-organisms in a beer using Nanopore sequencing + description_md: Identification of the micro-organisms in a beer using Nanopore sequencing + button_link: https://usegalaxy.eu/published/workflow?id=0590554db9794d13 + - title_md: WGS Part In "Analyses Of Metagenomics Data - The Global Picture" + description_md: WGS Part In "Analyses Of Metagenomics Data - The Global Picture" + button_link: https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 + - title_md: Taxonomic Profiling and Visualization of Metagenomic Data + description_md: Taxonomic Profiling and Visualization of Metagenomic Data + button_link: https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 + - title_md: Amplicon Tutorial + description_md: Amplicon Tutorial + button_link: https://usegalaxy.eu/published/workflow?id=565c989730f68362 + - title_md: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' + description_md: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' + button_link: https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 + - title_md: ' Cloud-Aerosole MT-MG Functional Profiling' + description_md: ' Cloud-Aerosole MT-MG Functional Profiling' + button_link: https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab + - title_md: Cloud-Aerosole MT-MG Reference Gene Catalog Building + description_md: Cloud-Aerosole MT-MG Reference Gene Catalog Building + button_link: https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 + - title_md: Cloud-Aerosole MT-MG Pre-Processing + description_md: Cloud-Aerosole MT-MG Pre-Processing + button_link: https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab + - title_md: Cloud Aerosol MT-MG Contamination Filtering + description_md: Cloud Aerosol MT-MG Contamination Filtering + button_link: https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab + - title_md: Cloud-Aerosole MT-MG Taxonomic Profiling + description_md: Cloud-Aerosole MT-MG Taxonomic Profiling + button_link: https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 + - id: tutorials title: Tutorials heading_md: > - - content: [] - - id: pathways - title: Learning pathways - heading_md: > - Connected tutorials to train you to perform microbial data analysis fast!. content: - - title_md: Introduction to Galaxy and Sequence analysis - description_md: > - New to Galaxy and/or the field of genomics? In this learing pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. - button_link: - - title_md: Metagenomics data processing and analysis for microbiome - description_md: > - - button_link: - - title_md: Clinical metaproteomics workflows within Galaxy - description_md: > - - button_link: - - - id: faq - title: FAQ - heading_md: > - - content: [] \ No newline at end of file + - title_md: Analyses of metagenomics data - The global picture + description_md: Analyses of metagenomics data - The global picture + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html + - title_md: Metatranscriptomics analysis using microbiome RNA-seq data + description_md: Metatranscriptomics analysis using microbiome RNA-seq data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html + - title_md: Pathogen detection from (direct Nanopore) sequencing data using Galaxy + - Foodborne Edition + description_md: Pathogen detection from (direct Nanopore) sequencing data using + Galaxy - Foodborne Edition + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html + - title_md: Metatranscriptomics analysis using microbiome RNA-seq data (short) + description_md: Metatranscriptomics analysis using microbiome RNA-seq data (short) + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html + - title_md: Taxonomic Profiling and Visualization of Metagenomic Data + description_md: Taxonomic Profiling and Visualization of Metagenomic Data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html + - title_md: Assembly of metagenomic sequencing data + description_md: Assembly of metagenomic sequencing data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html + - title_md: Antibiotic resistance detection + description_md: Antibiotic resistance detection + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html + - title_md: Building an amplicon sequence variant (ASV) table from 16S data using + DADA2 + description_md: Building an amplicon sequence variant (ASV) table from 16S data + using DADA2 + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html + - title_md: 16S Microbial analysis with Nanopore data + description_md: 16S Microbial analysis with Nanopore data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html + - title_md: Identification of the micro-organisms in a beer using Nanopore sequencing + description_md: Identification of the micro-organisms in a beer using Nanopore sequencing + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html + - title_md: QIIME 2 Moving Pictures + description_md: QIIME 2 Moving Pictures + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html + - title_md: Binning of metagenomic sequencing data + description_md: Binning of metagenomic sequencing data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html + - title_md: QIIME 2 Cancer Microbiome Intervention + description_md: QIIME 2 Cancer Microbiome Intervention + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html + - title_md: 16S Microbial Analysis with mothur (extended) + description_md: 16S Microbial Analysis with mothur (extended) + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html + - title_md: 16S Microbial Analysis with mothur (short) + description_md: 16S Microbial Analysis with mothur (short) + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html + - title_md: 16S Microbial analysis with Nanopore data + description_md: 16S Microbial analysis with Nanopore data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html \ No newline at end of file diff --git a/communities/microgalaxy/lab/sections/6_support_and_help.yml b/communities/microgalaxy/lab/sections/6_support_and_help.yml index cce7e489..b7b13db6 100644 --- a/communities/microgalaxy/lab/sections/6_support_and_help.yml +++ b/communities/microgalaxy/lab/sections/6_support_and_help.yml @@ -4,14 +4,16 @@ tabs: - id: help title: Help heading_md: > - You can browse through workflows before that have been reviewed by scientists. + You can request help trough different channels. If you think your problem might help other users as well, + please poste it in the Galaxy Help Forum. Please report tool bugs via the microGalaxy support and for + specific questions feel free to reach out via the matrix chat. content: - - title_md: Troubleshooting errors + - title_md: Troubleshooting description_md: > Find specific advice for {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) on the GTN. - - title_md: Galaxy [American/Australia/EU/France/..] Support + - title_md: Galaxy Help Forum description_md: > Any user of Galaxy [American/Australia/EU/France/..] can request support online! button_md: Request support @@ -41,8 +43,8 @@ tabs: [Privacy Policy]({{ data_policy_url }}) for information on your personal data and any data that you upload. - - id: request - title: Request + - id: increase-quota + title: Increase quota content: - title_md: How can I increase my storage quota? description_md: > diff --git a/communities/microgalaxy/lab/sections/7_community.yml b/communities/microgalaxy/lab/sections/7_community.yml index ed3cc8ca..e279857b 100644 --- a/communities/microgalaxy/lab/sections/7_community.yml +++ b/communities/microgalaxy/lab/sections/7_community.yml @@ -4,20 +4,12 @@ tabs: - id: participate title: Participate content: - - title_md: Chat with other users - description_md: > - Of course! Check out the microGalaxy Matrix channel - title_md: Join our community! description_md: > - This Galaxy space is the result of hard, collaborative work by many contributors . - It is maintained by the microGalaxy Community of Practice. - This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier. - Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)! - button_link: "{{ microgalaxy_matrix }}" button_md: button_tip: Visit microGalaxy diff --git a/communities/microgalaxy/lab/sections/tutorials_isolates_snippet.yml b/communities/microgalaxy/lab/sections/tutorials_isolates_snippet.yml new file mode 100644 index 00000000..2adb9cda --- /dev/null +++ b/communities/microgalaxy/lab/sections/tutorials_isolates_snippet.yml @@ -0,0 +1,139 @@ +content: + - title_md: Making sense of a newly assembled genome + description_md: Making sense of a newly assembled genome + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html + - title_md: Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina + MiSeq Data + description_md: Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina + MiSeq Data + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html + - title_md: Assembly of metagenomic sequencing data + description_md: Assembly of metagenomic sequencing data + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html + - title_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally + Illumina data) + description_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally + Illumina data) + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html + - title_md: Unicycler Assembly + description_md: Unicycler Assembly + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html + - title_md: Checking expected species and contamination in bacterial isolate + description_md: Checking expected species and contamination in bacterial isolate + button_link: + https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html + - title_md: Tree thinking for tuberculosis evolution and epidemiology + description_md: Tree thinking for tuberculosis evolution and epidemiology + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html + - title_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + description_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html + - title_md: Genome annotation with Prokka + description_md: Genome annotation with Prokka + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html + - title_md: Refining Genome Annotations with Apollo (prokaryotes) + description_md: Refining Genome Annotations with Apollo (prokaryotes) + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + - title_md: Identification of AMR genes in an assembled bacterial genome + description_md: Identification of AMR genes in an assembled bacterial genome + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html + - title_md: Bacterial Genome Annotation + description_md: Bacterial Genome Annotation + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html + - title_md: Comparative gene analysis in unannotated genomes + description_md: Comparative gene analysis in unannotated genomes + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html + - title_md: Essential genes detection with Transposon insertion sequencing + description_md: Essential genes detection with Transposon insertion sequencing + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html + - title_md: Genome annotation with Prokka + description_md: Genome annotation with Prokka + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html + - title_md: Making sense of a newly assembled genome + description_md: Making sense of a newly assembled genome + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html + - title_md: Microbial Variant Calling + description_md: Microbial Variant Calling + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html + - title_md: Refining Genome Annotations with Apollo (prokaryotes) + description_md: Refining Genome Annotations with Apollo (prokaryotes) + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + - title_md: Identification of AMR genes in an assembled bacterial genome + description_md: Identification of AMR genes in an assembled bacterial genome + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html + - title_md: Bacterial Genome Annotation + description_md: Bacterial Genome Annotation + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html + - title_md: Tree thinking for tuberculosis evolution and epidemiology + description_md: Tree thinking for tuberculosis evolution and epidemiology + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html + - title_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + description_md: 'Identifying tuberculosis transmission links: from SNPs to transmission + clusters' + button_link: + https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html + - title_md: M. tuberculosis Variant Analysis + description_md: M. tuberculosis Variant Analysis + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html + - title_md: Identification of AMR genes in an assembled bacterial genome + description_md: Identification of AMR genes in an assembled bacterial genome + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html + - title_md: 'metaQuantome 1: Data creation' + description_md: 'metaQuantome 1: Data creation' + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html + - title_md: Metaproteomics tutorial + description_md: Metaproteomics tutorial + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html + - title_md: 'metaQuantome 2: Function' + description_md: 'metaQuantome 2: Function' + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html + - title_md: 'metaQuantome 3: Taxonomy' + description_md: 'metaQuantome 3: Taxonomy' + button_link: + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html + - title_md: Quality and contamination control in bacterial isolate using Illumina + MiSeq Data + description_md: Quality and contamination control in bacterial isolate using Illumina + MiSeq Data + button_link: + https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html + - title_md: Calling variants in non-diploid systems + description_md: Calling variants in non-diploid systems + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html + - title_md: M. tuberculosis Variant Analysis + description_md: M. tuberculosis Variant Analysis + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html + - title_md: Microbial Variant Calling + description_md: Microbial Variant Calling + button_link: + https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html diff --git a/communities/microgalaxy/lab/sections/tutorials_microbiome_snippet.yml b/communities/microgalaxy/lab/sections/tutorials_microbiome_snippet.yml new file mode 100644 index 00000000..525a72b2 --- /dev/null +++ b/communities/microgalaxy/lab/sections/tutorials_microbiome_snippet.yml @@ -0,0 +1,69 @@ +content: + - title_md: Analyses of metagenomics data - The global picture + description_md: Analyses of metagenomics data - The global picture + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html + - title_md: Metatranscriptomics analysis using microbiome RNA-seq data + description_md: Metatranscriptomics analysis using microbiome RNA-seq data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html + - title_md: Pathogen detection from (direct Nanopore) sequencing data using Galaxy + - Foodborne Edition + description_md: Pathogen detection from (direct Nanopore) sequencing data using + Galaxy - Foodborne Edition + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html + - title_md: Metatranscriptomics analysis using microbiome RNA-seq data (short) + description_md: Metatranscriptomics analysis using microbiome RNA-seq data (short) + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html + - title_md: Taxonomic Profiling and Visualization of Metagenomic Data + description_md: Taxonomic Profiling and Visualization of Metagenomic Data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html + - title_md: Assembly of metagenomic sequencing data + description_md: Assembly of metagenomic sequencing data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html + - title_md: Antibiotic resistance detection + description_md: Antibiotic resistance detection + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html + - title_md: Building an amplicon sequence variant (ASV) table from 16S data using + DADA2 + description_md: Building an amplicon sequence variant (ASV) table from 16S data + using DADA2 + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html + - title_md: 16S Microbial analysis with Nanopore data + description_md: 16S Microbial analysis with Nanopore data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html + - title_md: Identification of the micro-organisms in a beer using Nanopore sequencing + description_md: Identification of the micro-organisms in a beer using Nanopore sequencing + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html + - title_md: QIIME 2 Moving Pictures + description_md: QIIME 2 Moving Pictures + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html + - title_md: Binning of metagenomic sequencing data + description_md: Binning of metagenomic sequencing data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html + - title_md: QIIME 2 Cancer Microbiome Intervention + description_md: QIIME 2 Cancer Microbiome Intervention + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html + - title_md: 16S Microbial Analysis with mothur (extended) + description_md: 16S Microbial Analysis with mothur (extended) + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html + - title_md: 16S Microbial Analysis with mothur (short) + description_md: 16S Microbial Analysis with mothur (short) + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html + - title_md: 16S Microbial analysis with Nanopore data + description_md: 16S Microbial analysis with Nanopore data + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html diff --git a/communities/microgalaxy/lab/sections/workflows_isolate_snippet.yml b/communities/microgalaxy/lab/sections/workflows_isolate_snippet.yml new file mode 100644 index 00000000..3052c0be --- /dev/null +++ b/communities/microgalaxy/lab/sections/workflows_isolate_snippet.yml @@ -0,0 +1,295 @@ +content: +- title_md: AMR-Pathfinder + description_md: AMR-Pathfinder + button_link: https://workflowhub.eu/workflows/1189?version=2 +- title_md: bacterial-genome-assembly/main + description_md: bacterial-genome-assembly/main 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confirmation' + description_md: '2: Plant virus confirmation' + button_link: https://workflowhub.eu/workflows/102?version=1 +- title_md: '1: Plant virus detection with kraken2 (SE)' + description_md: '1: Plant virus detection with kraken2 (SE)' + button_link: https://workflowhub.eu/workflows/124?version=1 +- title_md: '1: Plant virus detection with kraken2 (PE)' + description_md: '1: Plant virus detection with kraken2 (PE)' + button_link: https://workflowhub.eu/workflows/101?version=1 +- title_md: Halophiles workup of Comparative gene analysis + description_md: Halophiles workup of Comparative gene analysis + button_link: https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 +- title_md: pAllori Blood RNA + description_md: pAllori Blood RNA + button_link: https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 +- title_md: Metaproteomics workflow + description_md: Metaproteomics workflow + button_link: https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 +- title_md: 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Profiling and Visualization with Kron (release v0.1) + description_md: Taxonomy Profiling and Visualization with Kron (release v0.1) + button_link: https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b +- title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release + v0.1) + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + (release v0.1) + button_link: https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc +- title_md: Gene-based Pathogen Identification (release v0.1) + description_md: Gene-based Pathogen Identification (release v0.1) + button_link: https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 +- title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + button_link: https://usegalaxy.org/published/workflow?id=2d3063882d8239ff +- title_md: PathoGFAIR (imported from uploaded file) + 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(imported from uploaded file) + description_md: PathoGFAIR (imported from uploaded file) + button_link: https://usegalaxy.org.au/published/workflow?id=f5f9808fb50b6f2c +- title_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + description_md: Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation + button_link: https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4 +- title_md: Allele-based Pathogen Identification + description_md: Allele-based Pathogen Identification + button_link: https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad +- title_md: Gene-based Pathogen Identification + description_md: Gene-based Pathogen Identification + button_link: https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2 +- title_md: Taxonomy Profiling and Visualization with Krona + description_md: Taxonomy Profiling and Visualization with Krona + button_link: https://usegalaxy.org.au/published/workflow?id=d9ba165e6ae55417 +- title_md: Nanopore Preprocessing + description_md: Nanopore Preprocessing + button_link: https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b diff --git a/communities/microgalaxy/lab/sections/workflows_microbiome_snippet.yml b/communities/microgalaxy/lab/sections/workflows_microbiome_snippet.yml new file mode 100644 index 00000000..df646228 --- /dev/null +++ b/communities/microgalaxy/lab/sections/workflows_microbiome_snippet.yml @@ -0,0 +1,84 @@ +content: +- title_md: Taxonomy classification using Kraken2 and Bracken + description_md: Taxonomy classification using Kraken2 and Bracken + button_link: https://workflowhub.eu/workflows/1199?version=2 +- title_md: Analyses of shotgun metagenomics data with MetaPhlAn2 + description_md: Analyses of shotgun metagenomics data with MetaPhlAn2 + button_link: https://workflowhub.eu/workflows/624?version=1 +- title_md: 'Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]' + button_link: https://workflowhub.eu/workflows/653?version=1 +- title_md: 'Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]' + button_link: https://workflowhub.eu/workflows/652?version=1 +- title_md: 'Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]' + button_link: https://workflowhub.eu/workflows/651?version=1 +- title_md: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With + Mothur]' + description_md: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis + With Mothur]' + button_link: https://workflowhub.eu/workflows/650?version=1 +- title_md: 'Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]' + description_md: 'Workflow 1: Further Quality Control [16S Microbial Analysis With + Mothur]' + button_link: https://workflowhub.eu/workflows/648?version=1 +- title_md: 'Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis + With Mothur]' + description_md: 'Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis + With Mothur]' + button_link: https://workflowhub.eu/workflows/649?version=1 +- title_md: GTN Training - Antibiotic Resistance Detection + description_md: GTN Training - Antibiotic Resistance Detection + button_link: https://workflowhub.eu/workflows/406?version=1 +- title_md: pAllori Amplicon 16S Pre-Processing and Taxonomy Classification + description_md: pAllori Amplicon 16S Pre-Processing and Taxonomy Classification + button_link: https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 +- title_md: Cloud Aerosol MT-MG Contamination Filtering + description_md: Cloud Aerosol MT-MG Contamination Filtering + button_link: https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 +- title_md: Metatranscriptomics data analysis + description_md: Metatranscriptomics data analysis + button_link: https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 +- title_md: ' Cloud-Aerosole MT-MG Functional Profiling' + description_md: ' Cloud-Aerosole MT-MG Functional Profiling' + button_link: https://usegalaxy.eu/published/workflow?id=63478edcea3f449a +- title_md: Cloud-Aerosole MT-MG Pre-Processing + description_md: Cloud-Aerosole MT-MG Pre-Processing + button_link: https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 +- title_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + description_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + button_link: https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c +- title_md: Copy Of GTN Training - Antibiotic Resistance Detection + description_md: Copy Of GTN Training - Antibiotic Resistance Detection + button_link: https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa +- title_md: Identification of the micro-organisms in a beer using Nanopore sequencing + description_md: Identification of the micro-organisms in a beer using Nanopore sequencing + button_link: https://usegalaxy.eu/published/workflow?id=0590554db9794d13 +- title_md: WGS Part In "Analyses Of Metagenomics Data - The Global Picture" + description_md: WGS Part In "Analyses Of Metagenomics Data - The Global Picture" + button_link: https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 +- title_md: Taxonomic Profiling and Visualization of Metagenomic Data + description_md: Taxonomic Profiling and Visualization of Metagenomic Data + button_link: https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 +- title_md: Amplicon Tutorial + description_md: Amplicon Tutorial + button_link: https://usegalaxy.eu/published/workflow?id=565c989730f68362 +- title_md: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' + description_md: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' + button_link: https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 +- title_md: ' Cloud-Aerosole MT-MG Functional Profiling' + description_md: ' Cloud-Aerosole MT-MG Functional Profiling' + button_link: https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab +- title_md: Cloud-Aerosole MT-MG Reference Gene Catalog Building + description_md: Cloud-Aerosole MT-MG Reference Gene Catalog Building + button_link: https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 +- title_md: Cloud-Aerosole MT-MG Pre-Processing + description_md: Cloud-Aerosole MT-MG Pre-Processing + button_link: https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab +- title_md: Cloud Aerosol MT-MG Contamination Filtering + description_md: Cloud Aerosol MT-MG Contamination Filtering + button_link: https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab +- title_md: Cloud-Aerosole MT-MG Taxonomic Profiling + description_md: Cloud-Aerosole MT-MG Taxonomic Profiling + button_link: https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 diff --git a/sources/bin/populate_labs.sh b/sources/bin/populate_labs.sh new file mode 100644 index 00000000..d30c1fb4 --- /dev/null +++ b/sources/bin/populate_labs.sh @@ -0,0 +1,39 @@ +python sources/bin/populate_labs_workflows_toturials.py \ + --tsv communities/microgalaxy/resources/tutorials.tsv \ + --yml communities/microgalaxy/lab/sections/tutorials_isolates_snippet.yml \ + -tc Title \ + -dc Title \ + -blc Link \ + -fc Topic \ + -fi Microbiome \ + -fl exclude \ +&& \ +python sources/bin/populate_labs_workflows_toturials.py \ + --tsv communities/microgalaxy/resources/tutorials.tsv \ + --yml communities/microgalaxy/lab/sections/tutorials_microbiome_snippet.yml \ + -tc Title \ + -dc Title \ + -blc Link \ + -fc Topic \ + -fi Microbiome \ + -fl include \ +&& \ +python sources/bin/populate_labs_workflows_toturials.py \ + --tsv communities/microgalaxy/resources/workflows.tsv \ + --yml communities/microgalaxy/lab/sections/workflows_isolate_snippet.yml \ + -tc Name \ + -dc Name \ + -blc Link \ + -fc Tags \ + -fi "metagenomics, metatranscriptomics" \ + -fl exclude \ +&& \ +python sources/bin/populate_labs_workflows_toturials.py \ + --tsv communities/microgalaxy/resources/workflows.tsv \ + --yml communities/microgalaxy/lab/sections/workflows_microbiome_snippet.yml \ + -tc Name \ + -dc Name \ + -blc Link \ + -fc Tags \ + -fi "metagenomics, metatranscriptomics" \ + -fl include \ No newline at end of file diff --git a/sources/bin/populate_labs_tools.py b/sources/bin/populate_labs_tools.py new file mode 100644 index 00000000..9b2f943b --- /dev/null +++ b/sources/bin/populate_labs_tools.py @@ -0,0 +1,187 @@ +# python ./sources/bin/populate_labs.py --tool_tsv communities/microgalaxy/resources/curated_tools.tsv --tool_yml communities/microgalaxy/lab/sections/4_tools.yml + +import argparse +import os +from typing import List + +import pandas as pd +from ruamel.yaml import YAML as yaml +from ruamel.yaml.scalarstring import LiteralScalarString + +number_of_categories = 10 +number_of_tools = 10 + + +def add_tools_url(tools) -> None: + return tools + + +def main() -> None: + parser = argparse.ArgumentParser(description="Create community tools.yml from tool.tsv.") + + # Adding positional arguments with short options + parser.add_argument( + "-c", "--tool_tsv", type=str, required=True, help="Path to the TSV file (e.g., curated_tools.tsv)" + ) + parser.add_argument( + "-y", "--tool_yml", type=str, required=True, help="Path to the output YAML file (e.g., tools.yml)" + ) + + args = parser.parse_args() + + # Check if the tool TSV file exists + if not os.path.exists(args.tool_tsv): + print(f"Error: The file '{args.tool_tsv}' does not exist.") + return + + try: + # Read the TSV file with pandas (use tab delimiter) + tools = pd.read_csv(args.tool_tsv, sep="\t") + + # Construct the YAML data structure + yaml_data = { + "id": "tools", + "title": "Community curated tools", + "tabs": [], + } + + ################################# + # Add manual entry for tool request and complete list + ################################# + + entries = [] + + # Tool request + entry = { + "title_md": "Request a new tool", + "description_md": "You can request a new tool by contacting the microGalaxy community: microgalaxy@lists.galaxyproject.org", + } + entries.append(entry) + + # Complete tool list + entry = { + "title_md": "See the complete tool list", + "description_md": "Our comprehensive curated tool list is available via https://galaxyproject.github.io/galaxy_codex/microgalaxy", + } + entries.append(entry) + + # Add manual entries to the top of the tabs + yaml_data["tabs"].append( + { + "id": "more_tools", + "title": "More tools !", + "heading_md": f"Request a new tools or look at the complete list", + "content": entries, + } + ) + + ####################################### + # Get highest ranking EDAM operations + ####################################### + + count_column = "Suite runs on main servers" + + # Step 1: Split the categories into separate rows and strip whitespace + df = tools.assign(Category=tools["EDAM operations"].str.split(",")).explode("Category") + df["Category"] = df["Category"].str.strip() # Strip whitespace + + # Step 2: Group by category to calculate total count and item count + grouped = ( + df.groupby("Category") + .agg( + total_count=(count_column, "sum"), + item_count=("Suite ID", "size"), # Count distinct items if necessary, use 'nunique' + ) + .reset_index() + ) + + # Step 3: Filter categories with at least 5 items + filtered = grouped[grouped["item_count"] >= 5] + + ########################### + # Get the corresponding tools + ########################### + + # Step 4: Sort by total count in descending order + top_categories = filtered.sort_values(by="total_count", ascending=False).head(number_of_categories)["Category"] + + # Step 5: Assign each tool to the first category it appears in + # Sort by 'Galaxy wrapper id' to ensure we assign based on first appearance + df_unique = df[df["Category"].isin(top_categories)] # Filter rows for top 5 categories + df_unique = df_unique.sort_values(by=["Suite ID", "Category"]) # Sort by tool ID to keep first category only + + # Step 6: Remove duplicates, keeping the first appearance of each tool + df_unique = df_unique.drop_duplicates(subset=["Suite ID"], keep="first") + + # Step 7: Extract top 5 items per category based on total count + top_items_per_category = ( + df_unique.groupby("Category", group_keys=False) # Group by category + .apply(lambda group: group.nlargest(number_of_tools, count_column)) # Get top items per category + .reset_index(drop=True) # Reset index for clean output + ) + + ############################# + # Populate the table + ############################# + + for group_id, group in top_items_per_category.groupby("Category"): + + tool_entries = [] + for index, row in group.iterrows(): + + # Prepare the description with an HTML unordered list and links for each Galaxy tool ID + description = f"{row['Description']}\n (Tool usage: {row[count_column]})" + tool_ids = row["Tool IDs"] + owner = row["Suite owner"] + wrapper_id = row["Suite ID"] + + # Split the tool IDs by comma if it's a valid string, otherwise handle as an empty list + tool_ids_list = tool_ids.split(",") if isinstance(tool_ids, str) else [] + + # Create the base URL template for each tool link + url_template = ( + "/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2F{owner}%2F{wrapper_id}%2F{tool_id}" + ) + + # Build HTML list items with links + description += "\n" + + # Use LiteralScalarString to enforce literal block style for the description + description_md = LiteralScalarString(description.strip()) + + # Create the tool entry + tool_entry = { + "title_md": wrapper_id, + "description_md": description_md, + } + + tool_entries.append(tool_entry) + + # Create table entry for each EDAM + yaml_data["tabs"].append( + { + "id": group_id.replace(" ", "_").lower(), + "title": group_id, + "heading_md": f"Top 10 for the EDAM operation: {group_id}", + "content": tool_entries, + } + ) + + # Write the YAML data to the output file + with open(args.tool_yml, "w") as yaml_file: + yaml().dump(yaml_data, yaml_file) + print(f"Data successfully written to '{args.tool_yml}'") + + except Exception as e: + print(f"An error occurred: {e}") + + +if __name__ == "__main__": + main() diff --git a/sources/bin/populate_labs_workflows_toturials.py b/sources/bin/populate_labs_workflows_toturials.py new file mode 100644 index 00000000..f7a8c113 --- /dev/null +++ b/sources/bin/populate_labs_workflows_toturials.py @@ -0,0 +1,106 @@ +import argparse +import os +from typing import List, Dict, Any +import pandas as pd +from ruamel.yaml import YAML as yaml + + +def matches_filter(text: str, words: List[str], logic: str) -> bool: + """ + Determines if the given text matches the filter logic: + - 'include': Includes the text if it matches any word in the filter. + - 'exclude': Excludes the text if it matches any word in the filter. + + Args: + text (str): The text to check. + words (List[str]): A list of words to search for. + logic (str): The filter logic, either 'include' or 'exclude'. + + Returns: + bool: True if the text matches the filter logic, False otherwise. + """ + # Convert text and words to lowercase for case-insensitive comparison + text = text.lower() + words = [word.lower() for word in words] + + if logic == "include": + # Include if the text contains any word from the filter + return any(word in text for word in words) + + elif logic == "exclude": + # Exclude if the text contains any word from the filter + return not any(word in text for word in words) + + # Default to False if the logic is not recognized + return False + + +def main() -> None: + """ + Main function to create a YAML file from a TSV file based on specified filters and logic. + """ + # Initialize argument parser + parser = argparse.ArgumentParser(description="Create community *.yml from *.tsv.") + + # Define required arguments + parser.add_argument("-c", "--tsv", type=str, required=True, help="Path to the TSV file (e.g., curated_tools.tsv)") + parser.add_argument("-y", "--yml", type=str, required=True, help="Path to the output YAML file (e.g., tools.yml)") + + # Columns and filter details + parser.add_argument("-tc", "--title_column", type=str, required=True, help="Column to use as title.") + parser.add_argument("-dc", "--description_column", type=str, required=True, help="Column to use as description.") + parser.add_argument( + "-blc", "--button_link_column", type=str, required=True, help="Column to use as link for the button." + ) + parser.add_argument("-fc", "--filter_column", type=str, required=True, help="Column to use as filter.") + parser.add_argument( + "-fi", "--filter", type=str, required=True, help="Comma-separated list of words for filtering." + ) + parser.add_argument( + "-fl", "--filter_logic", type=str, required=True, choices=["include", "exclude"], + help="Specify the filter logic: 'include' to include matches, 'exclude' to exclude matches." + ) + + # Parse the arguments + args = parser.parse_args() + + # Check if the TSV file exists + if not os.path.exists(args.tsv): + print(f"Error: The file '{args.tsv}' does not exist.") + return + + try: + # Read the TSV file into a Pandas DataFrame + data_df: pd.DataFrame = pd.read_csv(args.tsv, sep="\t") + + # Initialize the YAML data structure + yaml_data: Dict[str, List[Dict[str, Any]]] = {"content": []} + + # Split the filter string into a list of words + filter_words = args.filter.split(",") + + # Iterate through each row in the DataFrame + for _index, row in data_df.iterrows(): + # Apply the filter logic + if matches_filter(str(row[args.filter_column]), filter_words, args.filter_logic): + # Only add rows that satisfy the filter logic + entry: Dict[str, Any] = { + "title_md": row[args.title_column], + "description_md": row[args.description_column], + "button_link": row[args.button_link_column], + } + yaml_data["content"].append(entry) + + # Write the constructed YAML data to the output file + with open(args.yml, "w") as yaml_file: + yaml().dump(yaml_data, yaml_file) + + print(f"Data successfully written to '{args.yml}'") + + except Exception as e: + # Handle any exceptions and print an error message + print(f"An error occurred: {e}") + + +if __name__ == "__main__": + main()