Try to fix YAML errors

galaxyproject · Jan 29, 2025 · e28138a · e28138a
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diff --git a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml
@@ -4,301 +4,6 @@ tabs:
 - id: workflows
   title: Workflows
   heading_md: ''
-  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: Tutorials to train you to perform microbial data analysis