diff --git a/.github/workflows/workflow-list.yaml b/.github/workflows/workflow-list.yaml new file mode 100644 index 00000000000000..1f14bfb8a9aa0c --- /dev/null +++ b/.github/workflows/workflow-list.yaml @@ -0,0 +1,53 @@ +name: "[Cron] Update Workflow List" +on: + workflow_dispatch: + schedule: + - cron: '45 0 * * 2' +jobs: + runner-job: + runs-on: ubuntu-latest + # Only run on main repo on and PRs that match the main repo. + if: | + github.repository == 'galaxyproject/training-material' && + (github.event_name != 'pull_request' || + github.event.pull_request.head.repo.full_name == github.repository) + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 10 + + # BEGIN Dependencies + - uses: ruby/setup-ruby@v1 + with: + ruby-version: "3.0" + - uses: actions/cache@v2 + with: + path: | + vendor/bundle + key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }} + restore-keys: | + ${{ runner.os }}-gems- + - name: Install dependencies + run: | + gem install bundler + bundle config path vendor/bundle + bundle install --jobs 4 --retry 3 + bundle pristine ffi + # END Dependencies + + - name: Update Shortlinks + id: generate + run: | + echo "new_ids=$(ruby bin/workflows-fetch.rb)" >> $GITHUB_OUTPUT + + - name: Create Pull Request + # If it's not a Pull Request then commit any changes as a new PR. + if: | + github.event_name != 'pull_request' && + steps.generate.outputs.new_ids != '' + uses: peter-evans/create-pull-request@v3 + with: + title: Update Persistent uniform resource locators + branch-suffix: timestamp + commit-message: Update PURLs + add-paths: metadata/workflows.yaml diff --git a/bin/workflows-fetch.rb b/bin/workflows-fetch.rb index 369175008e415a..e7dbb38b735cbd 100755 --- a/bin/workflows-fetch.rb +++ b/bin/workflows-fetch.rb @@ -4,16 +4,22 @@ require 'uri' require 'yaml' -# Get the list of workflows -def fetch_workflows(server) - uri = URI.parse("#{server}/api/workflows/") +def request(url) + uri = URI.parse(url) request = Net::HTTP::Get.new(uri) + request['Accept'] = 'application/json' req_options = { use_ssl: uri.scheme == 'https', } response = Net::HTTP.start(uri.hostname, uri.port, req_options) do |http| http.request(request) end + response +end + +# Get the list of workflows +def fetch_workflows(server) + response = request("#{server}/api/workflows/") begin JSON.parse(response.body).map do |w| @@ -25,10 +31,67 @@ def fetch_workflows(server) end end +def fetch_workflowhub() + projects = JSON.parse(request("https://workflowhub.eu/projects").body) + project_mapping = projects['data'].map{|p| [p['id'], p['attributes']['title']]}.to_h + + response = request("https://workflowhub.eu/workflows?filter[workflow_type]=galaxy") + data = JSON.parse(response.body) + if !data['links']['next'].nil? + puts "ERROR: Cannot yet handle multiple pages" + exit 42 + end + puts "INFO: Fetching #{data['data'].length} workflows from WorkflowHub" + data['data'].map.with_index { |w, i| + # {"id"=>"14", "type"=>"workflows", "attributes"=>{"title"=>"Cheminformatics - Docking"}, "links"=>{"self"=>"/workflows/14"}} + wf_info = JSON.parse(request("https://workflowhub.eu#{w['links']['self']}").body) + creator_list = [] + + creator0 = wf_info['data']['attributes']['creators'][0] + owner = "" + if !creator0.nil? + # Primary + creator_list.push(creator0['given_name'] + " " + creator0['family_name']) + else + # Other creators + other = wf_info['data']['attributes']['other_creators'] + if !other.nil? && other.length.positive? + creator_list.push(wf_info['data']['attributes']['other_creators'].split(',').map{|x| x.strip}) + else + end + end + # Projects + wf_info['data']['relationships']['projects']['data'].each do |p| + creator_list.push(project_mapping[p['id']]) + end + + creator_list = creator_list.flatten.compact.uniq + + begin + r = { + 'name' => wf_info['data']['attributes']['title'], + 'owner' => creator_list.join(', '), + 'number_of_steps' => wf_info['data']['attributes']['internals']['steps'].length, + 'server' => 'https://workflowhub.eu', + 'id' => wf_info['data']['id'], + 'tags' => wf_info['data']['attributes']['tags'].map{|t| t.gsub(/^name:/, '')}, + 'update_time' => wf_info['data']['attributes']['updated_at'], + } + rescue + r = nil + end + r + }.reject{|x| x.nil? } +end + + # Parse the response workflows_eu = fetch_workflows('https://usegalaxy.eu') -workflows_org = fetch_workflows('https://usegalaxy.org') -workflows_aus = fetch_workflows('https://usegalaxy.org.au') +puts "INFO: Fetched #{workflows_eu.length} workflows from EU" +workflows_org = fetch_workflows("https://usegalaxy.org") +puts "INFO: Fetched #{workflows_org.length} workflows from ORG" +workflows_aus = fetch_workflows("https://usegalaxy.org.au") +puts "INFO: Fetched #{workflows_aus.length} workflows from AUS" workflows = workflows_eu + workflows_org + workflows_aus # Cleanup the list @@ -36,6 +99,9 @@ def fetch_workflows(server) w['published'] == true && w['importable'] == true && w['deleted'] == false && w['hidden'] == false end +# Add in WFHub workflows +workflows += fetch_workflowhub() + # Group by name + owner cleaned = workflows.group_by { |w| "#{w['name']}#{w['owner']}" } cleaned = cleaned.map do |_k, v| diff --git a/metadata/workflows.yml b/metadata/workflows.yml new file mode 100644 index 00000000000000..743cc7b7c70b22 --- /dev/null +++ b/metadata/workflows.yml @@ -0,0 +1,22363 @@ +--- +- name: Average Bigwig between replicates (release v0.2) + owner: iwc + steps: 4 + ids: + - - https://usegalaxy.eu + - f53b5a60763d85b6 + - - https://usegalaxy.org + - 36a32a845cdeb93e + tags: [] + updated: '2023-10-05T00:10:58.845932' +- name: ATACseq (release v0.6) + owner: iwc + steps: 30 + ids: + - - https://usegalaxy.eu + - d12617d0df5f81d0 + - - https://usegalaxy.org + - b63d1e1024cc3295 + tags: + - ATACseq + updated: '2023-10-05T00:10:52.105737' +- name: Parallel Accession Down (release v0.1.6) + owner: iwc + steps: 6 + ids: + - - https://usegalaxy.eu + - 6478043c474ac82e + - - https://usegalaxy.org + - 278c8f376de66bd7 + - - https://usegalaxy.org.au + - 97016c7546583e3d + tags: [] + updated: '2023-10-05T00:11:09.149633' +- name: WF4_Quantitation_Workflow + owner: pratikjagtap + steps: 14 + ids: + - - https://usegalaxy.eu + - 0dc600f6cce9a335 + tags: [] + updated: '2023-10-03T21:31:26.417551' +- name: WF3-Verification Workflow + owner: pratikjagtap + steps: 21 + ids: + - - https://usegalaxy.eu + - bbfabbc3e4bcc73d + tags: [] + updated: '2023-10-03T21:24:43.181573' +- name: WF2_Discovery-Workflow + owner: pratikjagtap + steps: 27 + ids: + - - https://usegalaxy.eu + - 607ca3a9d45bd080 + tags: [] + updated: '2023-10-03T21:14:13.225882' +- name: WF1_Database Generation Workflow + owner: pratikjagtap + steps: 7 + ids: + - - https://usegalaxy.eu + - 2f7e13eb26c8cd18 + tags: [] + updated: '2023-10-03T21:00:59.614266' +- name: WF5_Data-interpretation-worklow + owner: pratikjagtap + steps: 11 + ids: + - - https://usegalaxy.eu + - d148459a4d4b91f1 + tags: [] + updated: '2023-10-03T18:40:47.062414' +- name: Average Bigwig between replicates (release v0.1) + owner: iwc + steps: 4 + ids: + - - https://usegalaxy.eu + - 3b1f0473ec89aa00 + - - https://usegalaxy.org + - 8bd051791178953a + tags: [] + updated: '2023-09-28T00:11:09.798462' +- name: Repeat masking with RepeatModeler and RepeatMask (release v0.1) + owner: iwc + steps: 3 + ids: + - - https://usegalaxy.eu + - '09c534f738426a6d' + - - https://usegalaxy.org + - effc17e170263ae6 + - - https://usegalaxy.org.au + - ffb1117077f68a9f + tags: [] + updated: '2023-09-28T00:13:22.650808' +- name: ATACseq (release v0.5.1) + owner: iwc + steps: 30 + ids: + - - https://usegalaxy.eu + - 8132c3b710fd6d48 + - - https://usegalaxy.org + - 8a215695e7b57cf5 + tags: + - ATACseq + updated: '2023-09-28T00:11:00.578416' +- name: Hi-C_fastqToPairs_hic (release v0.3) + owner: iwc + steps: 9 + ids: + - - https://usegalaxy.eu + - cbe9e09ed3e91e2e + - - https://usegalaxy.org + - 2ffae50d0916b641 + tags: + - Hi-C + updated: '2023-09-21T00:10:39.109158' +- name: RNAseq_PE (release v0.4.1) + owner: iwc + steps: 27 + ids: + - - https://usegalaxy.eu + - 6ebd09100fc98878 + - - https://usegalaxy.org + - 53fdff74729a6780 + tags: + - RNAseq + updated: '2023-09-21T00:10:30.402808' +- name: RNAseq_PE (release v0.5) + owner: iwc + steps: 21 + ids: + - - https://usegalaxy.eu + - 406e6ef0dfb38628 + - - https://usegalaxy.org + - 2f774500d5bec9a6 + tags: + - RNAseq + updated: '2023-09-21T00:10:27.548381' +- name: RNAseq_SR (release v0.4.1) + owner: iwc + steps: 25 + ids: + - - https://usegalaxy.eu + - d3edc3f0659a5e5b + - - https://usegalaxy.org + - 3e6c9ab5ef3250ae + tags: + - RNAseq + updated: '2023-09-21T00:10:24.116875' +- name: RNAseq_SR (release v0.5) + owner: iwc + steps: 20 + ids: + - - https://usegalaxy.eu + - bace9aebab9d4ce3 + - - https://usegalaxy.org + - 63b3b266bde77563 + tags: + - RNAseq + updated: '2023-09-21T00:10:21.259004' +- name: 'imported: EBI SC Expression Atlas Release 19 Analysis Pipeline v0.2.5 (Scanpy + 1.8.1 - droplet)' + owner: wendi.bacon + steps: 45 + ids: + - - https://usegalaxy.eu + - f562ce57c48f3a93 + tags: [] + updated: '2023-09-20T13:00:19.362458' +- name: Arquea workflow + owner: mruizvillarrazo + steps: 15 + ids: + - - https://usegalaxy.eu + - 51cce3b98da3e822 + tags: [] + updated: '2023-09-20T09:10:33.443093' +- name: RasgosFlow + owner: mruizvillarrazo + steps: 12 + ids: + - - https://usegalaxy.eu + - 7878623b7e959284 + tags: [] + updated: '2023-09-19T10:57:50.378746' +- name: Inferring Trajectories with Scanpy Tutorial Workflow + owner: marisa_jl + steps: 16 + ids: + - - https://usegalaxy.eu + - decd6ad0b41289ef + tags: + - name:singlecell + updated: '2023-09-19T09:37:21.181027' +- name: AMR detection workflow - CFIA + owner: dennisd + steps: 13 + ids: + - - https://usegalaxy.eu + - ca0c02997d948113 + - - https://usegalaxy.eu + - 70f7daacf58658db + tags: [] + updated: '2023-09-18T11:18:39.659223' +- name: 'imported: Inferring Trajectories with Scanpy Tutorial Workflow' + owner: wendi.bacon + steps: 16 + ids: + - - https://usegalaxy.eu + - df336dc72c35ecdc + tags: + - name:singlecell + updated: '2023-09-14T15:42:44.498823' +- name: Assembly polishing with long reads (release v0.1) + owner: iwc + steps: 11 + ids: + - - https://usegalaxy.eu + - a4f50449afde4a05 + - - https://usegalaxy.org + - bcdc5ce2ea8700fc + - - https://usegalaxy.org.au + - 0c421197e022f323 + tags: [] + updated: '2023-09-14T00:11:59.002298' +- name: Workflow constructed from history 'LSDV analysis development' + owner: akkm4187 + steps: 9 + ids: + - - https://usegalaxy.eu + - 3fb550d7c2bc390a + tags: [] + updated: '2023-09-13T03:35:27.734863' +- name: Clinical-MP-Database generation + owner: subina + steps: 14 + ids: + - - https://usegalaxy.eu + - c6aecbdbeb27585f + tags: [] + updated: '2023-09-07T16:50:17.607815' +- name: Get Confident Peaks From ATAC or CUTandRUN duplicates (release v0.1) + owner: iwc + steps: 20 + ids: + - - https://usegalaxy.eu + - 5385abe9c2589b69 + - - https://usegalaxy.org + - 23468eea382e6bb4 + tags: + - ChIP + updated: '2023-09-07T00:10:56.186884' +- name: Get Confident Peaks From ChIP_PE duplicates (release v0.1) + owner: iwc + steps: 20 + ids: + - - https://usegalaxy.eu + - 16080c3c1488a8b5 + - - https://usegalaxy.org + - 6dcb43f86b9cd7dc + tags: + - ChIP + updated: '2023-09-07T00:10:53.882347' +- name: Get Confident Peaks From ChIP_SR duplicates (release v0.1) + owner: iwc + steps: 20 + ids: + - - https://usegalaxy.eu + - 0fb12e3a127fc4be + - - https://usegalaxy.org + - 6a2dace98986992a + tags: + - ChIP + updated: '2023-09-07T00:10:51.519762' +- name: Hi-C_juicermediumtabixToCool_c (release v0.2.1) + owner: iwc + steps: 7 + ids: + - - https://usegalaxy.eu + - 1214523f54a999fc + - - https://usegalaxy.org + - a93eb877596ce0ef + tags: + - Hi-C + updated: '2023-09-07T00:10:49.101974' +- name: Hi-C_fastqToPairs_hic (release v0.2) + owner: iwc + steps: 9 + ids: + - - https://usegalaxy.eu + - 7d49f41cd294e15b + - - https://usegalaxy.org + - 748c1a9d85eb61e2 + tags: + - Hi-C + updated: '2023-09-07T00:10:46.952524' +- name: Hi-C_juicermediumtabixToCool_c (release v0.2) + owner: iwc + steps: 7 + ids: + - - https://usegalaxy.eu + - fc4e3479d86f9a26 + - - https://usegalaxy.org + - 1e4eb6ccb47d9fc7 + tags: + - Hi-C + updated: '2023-09-07T00:10:44.756459' +- name: cHi-C_fastqToCool_hicup_c (release v0.2) + owner: iwc + steps: 17 + ids: + - - https://usegalaxy.eu + - 9f8a93cfffb31cd6 + - - https://usegalaxy.org + - f80b80aa7fb196ba + tags: + - Hi-C + updated: '2023-09-07T00:10:42.514468' +- name: Hi-C_fastqToCool_hicup_c (release v0.2) + owner: iwc + steps: 12 + ids: + - - https://usegalaxy.eu + - 506a451679fe25b4 + - - https://usegalaxy.org + - 0bc1b8888d8b20c4 + tags: + - Hi-C + updated: '2023-09-07T00:10:39.699636' +- name: Hi-C_fastqToPairs_hic (release v0.2.1) + owner: iwc + steps: 9 + ids: + - - https://usegalaxy.eu + - 83fea2e4508bc3ed + - - https://usegalaxy.org + - ba4815ec62edab04 + tags: + - Hi-C + updated: '2023-09-07T00:10:37.071011' +- name: cHi-C_fastqToCool_hicup_c (release v0.2.1) + owner: iwc + steps: 17 + ids: + - - https://usegalaxy.eu + - f394d1b12779ba41 + - - https://usegalaxy.org + - 7353afb9301780e5 + tags: + - Hi-C + updated: '2023-09-07T00:10:34.709631' +- name: Hi-C_fastqToCool_hicup_c (release v0.2.1) + owner: iwc + steps: 12 + ids: + - - https://usegalaxy.eu + - 72201ffaf488f278 + - - https://usegalaxy.org + - 4998f171ec922c7d + tags: + - Hi-C + updated: '2023-09-07T00:10:31.985409' +- name: ATACseq (release v0.5) + owner: iwc + steps: 29 + ids: + - - https://usegalaxy.eu + - 54b91dd86f463391 + - - https://usegalaxy.org + - b5e8f4a0ff226921 + tags: + - ATACseq + updated: '2023-09-07T00:10:29.217188' +- name: CUTandRUN (release v0.4) + owner: iwc + steps: 15 + ids: + - - https://usegalaxy.eu + - 146cef3acb2eba75 + - - https://usegalaxy.org + - 67992bf894a82587 + - - https://usegalaxy.org.au + - 2f520cb446adf726 + tags: + - CUTnRUN + updated: '2023-09-07T00:11:44.421393' +- name: Parallel Accession Down (release v0.1.4) + owner: iwc + steps: 6 + ids: + - - https://usegalaxy.eu + - '08e50a41a8571c15' + - - https://usegalaxy.org + - 4dfe253e26b29052 + - - https://usegalaxy.org.au + - 367116498fc5d46b + tags: [] + updated: '2023-09-07T00:11:04.641021' +- name: sequence mapping + owner: yiqundu + steps: 0 + ids: + - - https://usegalaxy.eu + - 996b0499d98b1869 + tags: [] + updated: '2023-09-06T18:39:42.935964' +- name: WGS Illumina for Microbiome (comprehensive) + owner: rahadian.pratama + steps: 12 + ids: + - - https://usegalaxy.eu + - 007ce6405d196df3 + tags: [] + updated: '2023-09-03T06:38:23.127899' +- name: Exploring Iris dataset with statistics and scatterplots + owner: itisalirh + steps: 9 + ids: + - - https://usegalaxy.eu + - 204854b8ec94da85 + tags: [] + updated: '2023-09-01T10:51:17.394021' +- name: Hi-C_fastqToPairs_hic (release v0.1) + owner: iwc + steps: 9 + ids: + - - https://usegalaxy.eu + - 57b96a59cca0e8df + - - https://usegalaxy.org + - 43cea919ebf9d978 + tags: + - Hi-C + updated: '2023-08-31T08:42:59.522233' +- name: ChIPseq_SR (release v0.4) + owner: iwc + steps: 12 + ids: + - - https://usegalaxy.eu + - fa0ff9a0db8bbddb + - - https://usegalaxy.org + - 90ed607bedd65524 + - - https://usegalaxy.org.au + - b8968fb0bf796e53 + - - https://usegalaxy.org.au + - 1ff259845498b818 + tags: + - ChIP + updated: '2023-09-07T00:11:53.834765' +- name: ChIPseq_PE (release v0.4) + owner: iwc + steps: 13 + ids: + - - https://usegalaxy.eu + - fd6429a788660c8d + - - https://usegalaxy.org + - cb011900fc0ee12a + - - https://usegalaxy.org.au + - 48a25f8e58d068e6 + - - https://usegalaxy.org.au + - 8433a2f79b2e5894 + tags: + - ChIP + updated: '2023-09-07T00:11:47.885216' +- name: Pathogen-Detection-Nanopore-All-Samples-Analysis + owner: engy.nasr + steps: 64 + ids: + - - https://usegalaxy.eu + - c8bc4af6dd3b5d02 + tags: + - microbiome + - nanopore + - IWC + - name:Collection + updated: '2023-08-29T21:12:27.992842' +- name: Pathogen-Detection-Nanopore-Pre-Processing + owner: engy.nasr + steps: 25 + ids: + - - https://usegalaxy.eu + - a705370bc2c13d5c + - - https://usegalaxy.eu + - 889f2782ad82bd69 + tags: + - microbiome + - nanopore + - IWC + - name:Collection + updated: '2023-08-29T15:07:43.668078' +- name: CONCOCT + owner: berenice + steps: 11 + ids: + - - https://usegalaxy.eu + - 58f779d238d569dc + tags: [] + updated: '2023-08-28T07:21:50.507784' +- name: Pathogen-Detection-Nanopore-SNP-based-pathogenetic-Identification + owner: engy.nasr + steps: 9 + ids: + - - https://usegalaxy.eu + - '09c7069ae409c362' + - - https://usegalaxy.eu + - 3f0b104a74acf869 + tags: + - microbiome + - nanopore + - IWC + - name:Collection + updated: '2023-08-27T08:15:02.357218' +- name: Pathogen-Detection-Nanopore-Taxonomy-Profiling-and-Visualization-with-Krona + owner: engy.nasr + steps: 5 + ids: + - - https://usegalaxy.eu + - 10101558b211a782 + tags: + - microbiome + - nanopore + - IWC + - name:Collection + updated: '2023-08-24T10:16:38.260205' +- name: test_cond_wf_short + owner: polina + steps: 5 + ids: + - - https://usegalaxy.eu + - 9f3a6237aa09f3cb + tags: [] + updated: '2023-08-22T10:57:23.311133' +- name: Pathogen-Detection-Nanopore-Gene-based-pathogenic-Identification + owner: engy.nasr + steps: 23 + ids: + - - https://usegalaxy.eu + - 585c21b7b1d864fc + - - https://usegalaxy.eu + - 2b888e200dfd91bc + tags: + - microbiome + - nanopore + - IWC + - name:Collection + updated: '2023-08-20T16:37:33.727585' +- name: Nanopore genome sequencing (viridiplantae) + owner: rahadian.pratama + steps: 6 + ids: + - - https://usegalaxy.eu + - 34a07bf6407510ef + tags: + - WGS + - Nanopore + updated: '2023-08-20T07:41:42.144907' +- name: GPU_Jupyterlab_tool_workflow + owner: kumara + steps: 6 + ids: + - - https://usegalaxy.eu + - cc483bb070e57474 + tags: [] + updated: '2023-08-17T09:36:54.216171' +- name: main + owner: microfuge1 + steps: 3 + ids: + - - https://usegalaxy.eu + - 533700cbfc4988c3 + tags: [] + updated: '2023-08-08T15:28:27.773257' +- name: peaks to genes + owner: vazhappilly + steps: 4 + ids: + - 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- https://usegalaxy.org + - 121f37a5c0562f8c + tags: [] + updated: '2015-01-26T02:48:26.200247' +- name: Tumor FFPE aligned BAM file with GATK and without GATK + owner: umar + steps: 15 + ids: + - - https://usegalaxy.org + - ca5ca2f38c1719e1 + tags: [] + updated: '2015-01-26T02:46:53.318240' +- name: Workflow constructe gnene lens + owner: rbroni + steps: 4 + ids: + - - https://usegalaxy.org + - 13a550ed56b56502 + tags: [] + updated: '2015-01-20T16:01:54.957663' +- name: Riboseq processing workflow + owner: rlegendre + steps: 6 + ids: + - - https://usegalaxy.org + - b0a12221ce09c001 + tags: [] + updated: '2015-01-15T15:07:32.168903' +- name: Standard strict virus mapping + owner: jules-hiscox + steps: 6 + ids: + - - https://usegalaxy.org + - 3d1f4bd67ce30f99 + tags: [] + updated: '2014-12-09T17:19:35.764279' +- name: pre-processing_final project + owner: mabelwang21 + steps: 14 + ids: + - - https://usegalaxy.org + - e6838c861b6beaed + tags: [] + updated: '2014-12-04T18:11:06.832484' +- name: 'imported: ChIP-seq control hg38, create BAM for control samples (INPUT, IgG, + etc.)' + owner: faizaan + steps: 5 + ids: + - - https://usegalaxy.org + - 4aad96570d252f95 + tags: [] + updated: '2014-12-01T21:33:08.753537' +- name: RNA-Seq Mapping + owner: ralonso + steps: 4 + ids: + - - https://usegalaxy.org + - 846b6fa2b8e20c3c + tags: [] + updated: '2014-11-25T10:04:02.751128' +- name: ChIP-seq workflow + owner: ralonso + steps: 3 + ids: + - - https://usegalaxy.org + - dcb73fce390b36b2 + tags: [] + updated: '2014-11-25T10:03:53.197614' +- name: 'imported: SNP calls (bwa-unified genotyper)' + owner: ralonso + steps: 3 + ids: + - - https://usegalaxy.org + - 4da3871ed87e8f21 + tags: [] + updated: '2014-11-25T10:02:28.904462' +- name: Kumova Problem Set + owner: okumova + steps: 17 + ids: + - - https://usegalaxy.org + - bad9b88a6d5b6759 + tags: [] + updated: '2014-11-04T16:09:46.233748' +- name: Coding Exons with the largest number of Simple Repeats + owner: judys15 + steps: 5 + ids: + - - https://usegalaxy.org + - 433a71f7f2d17834 + tags: [] + updated: '2014-10-26T21:05:06.412325' +- name: Workflow constructed from history 'TP Galaxy' + owner: youssef-barhoun + steps: 15 + ids: + - - https://usegalaxy.org + - c3b3b2ee14bbd374 + tags: [] + updated: '2014-10-22T15:21:09.800642' +- name: Workflow constructed from history 'GALAXY workshop' + owner: kuhaoura + steps: 9 + ids: + - - https://usegalaxy.org + - eb20150175a6ab03 + tags: [] + updated: '2014-10-13T11:43:03.137240' +- name: Workflow constructed from history 'galaxyWorkshop' + owner: zikozak92 + steps: 10 + ids: + - - https://usegalaxy.org + - 1b385fd45ee48614 + tags: [] + updated: '2014-10-13T11:41:54.121777' +- name: SNP calls (bwa-unified genotyper) + owner: dan-lawson + steps: 3 + ids: + - - https://usegalaxy.org + - 173def229790fbee + tags: [] + updated: '2014-09-30T19:28:02.621555' +- name: Galaxy 101 + owner: gabrieledani + steps: 7 + ids: + - - https://usegalaxy.org + - b11171cc4ccd84c7 + tags: [] + updated: '2014-09-11T18:14:48.426579' +- name: linkY - discover Y-linked genes from RNASeq data; testtoolshed.g2.bx.psu.edu/view/biomonika/linkyx + owner: biomonika + steps: 37 + ids: + - - https://usegalaxy.org + - 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55aa743125c2465d + tags: + - metagenomics + - galaxy + - NGS + - Metagenomics + updated: '2014-08-20T02:16:06.080338' +- name: Rnbeads + owner: ethan + steps: 0 + ids: + - - https://usegalaxy.org + - 4c6497b245d9c414 + tags: [] + updated: '2014-07-01T11:30:37.401508' +- name: Fasta labeled by identifiers + owner: jen + steps: 4 + ids: + - - https://usegalaxy.org + - a808c139402d7b87 + tags: + - fasta + - reformat + - identifiers + - datasets + updated: '2014-06-26T17:17:33.591315' +- name: RNAseq with rRNA removal + owner: nikiloo + steps: 19 + ids: + - - https://usegalaxy.org + - b2176abeb937f026 + tags: [] + updated: '2014-06-23T06:02:11.502033' +- name: Unnamed workflow + owner: biomnis + steps: 5 + ids: + - - https://usegalaxy.org + - 67c2ca24bc0be58e + tags: [] + updated: '2014-06-19T14:04:40.393960' +- name: MGEScan - identifying long terminal repeats (LTR) and non-LTR retroelements + in eukaryotic genomic sequences + owner: hyungro-lee + steps: 6 + ids: + - - https://usegalaxy.org + - a8df35c2754f2aa3 + tags: [] + updated: '2014-06-17T19:10:51.485376' +- name: Unnamed workflow + owner: lukeliu1991 + steps: 5 + ids: + - - https://usegalaxy.org + - 72f92e14f4b61c68 + tags: [] + updated: '2014-06-15T18:01:08.868695' +- name: Subtracting strains from VCF uwml + owner: chapinh + steps: 5 + ids: + - - https://usegalaxy.org + - e77c09c72dfaa9a4 + tags: [] + updated: '2014-06-03T16:45:26.029432' +- name: VCF to snpeffs uwml + owner: chapinh + steps: 2 + ids: + - - https://usegalaxy.org + - cb153c8d1685de3b + tags: [] + updated: '2014-06-03T16:44:40.396282' +- name: Workflow constructed from history 'Extract Workflow' + owner: galaxyproject + steps: 12 + ids: + - - https://usegalaxy.org + - 9cc814d43379c2a6 + tags: [] + updated: '2014-05-13T03:06:35.537112' +- name: Workflow constructed from history 'Tutorial (Yodosha, 2014)' + owner: kawaji + steps: 7 + ids: + - - https://usegalaxy.org + - e4f6b68301aafd38 + tags: [] + updated: '2014-05-08T05:17:24.209472' +- name: Unnamed workflow + owner: ingang + steps: 0 + ids: + - - https://usegalaxy.org + - f55eef988605523e + tags: [] + updated: '2014-05-07T02:10:21.981438' +- name: Genome Coverage Histogram + owner: bradlanghorst + steps: 9 + ids: + - - https://usegalaxy.org + - 67080f040e855990 + tags: [] + updated: '2014-05-06T23:37:23.332582' +- name: HW5(Huvec) + owner: '' + steps: 8 + ids: + - - https://usegalaxy.org + - 02d49c5f0d9aa010 + tags: [] + updated: '2014-04-29T17:44:40.274481' +- name: HW5(GM20000) + owner: '' + steps: 9 + ids: + - - https://usegalaxy.org + - 8356ee639055cbca + tags: [] + updated: '2014-04-29T17:44:40.273745' +- name: HW4(2) + owner: '' + steps: 2 + ids: + - - https://usegalaxy.org + - 244cf7723892cac4 + tags: [] + updated: '2014-04-29T17:44:40.271508' +- name: Homework 4 part 2 + owner: niraj + steps: 3 + ids: + - - https://usegalaxy.org + - 4be28cd3b398e0d6 + tags: [] + updated: '2014-04-29T17:44:40.269802' +- name: HW4 + owner: '' + steps: 5 + ids: + - - https://usegalaxy.org + - b9e3676a84b7be5d + tags: [] + updated: '2014-04-29T17:44:40.267809' +- name: Homework 4 + owner: niraj + steps: 5 + ids: + - - https://usegalaxy.org + - 4703371e94b67347 + tags: [] + updated: '2014-04-29T17:44:40.266089' +- name: HW5-Fetch + owner: '' + steps: 2 + ids: + - - https://usegalaxy.org + - 6471aa8abbb3fa40 + tags: [] + updated: '2014-04-25T23:09:06.763526' +- name: Workflow constructed from history 'Exercise 1' + owner: lindab + steps: 4 + ids: + - - https://usegalaxy.org + - a1333d6d9af28547 + tags: [] + updated: '2014-04-22T08:12:08.215733' +- name: 'Constructed Workflow ' + owner: james + steps: 4 + ids: + - - https://usegalaxy.org + - 013bf76cb3a8bd66 + tags: [] + updated: '2014-03-27T21:52:38.485256' +- name: workflow2 + owner: touzet + steps: 25 + ids: + - - https://usegalaxy.org + - 0b3af7e9ac69a6b7 + tags: [] + updated: '2014-03-25T10:33:40.464161' +- name: 'imported: FastQ to High Quality, Filtered, Headered, Sorted BAM (imported + from uploaded file)' + owner: elizar + steps: 3 + ids: + - - https://usegalaxy.org + - 378159d1ad2e98f9 + tags: [] + updated: '2014-03-19T17:52:01.479441' +- name: Bristol workflow to get sorted unique proper pair mapped reads + owner: davidmatthews + steps: 11 + ids: + - - https://usegalaxy.org + - 1e2e064c33b9c521 + tags: + - rna + - seq + - sam + - paired + - unique + updated: '2014-03-19T07:36:34.170699' +- name: Exome Analysis + owner: jeremy + steps: 11 + ids: + - - https://usegalaxy.org + - a7a145c196aa55c9 + tags: + - Exome + - exome + - workflow + updated: '2014-03-17T14:31:11.481716' +- name: CloudMap Variant Discovery Mapping (and Variant Calling) workflow _2-7-2014 + owner: gm2123 + steps: 33 + ids: + - - https://usegalaxy.org + - 83fbcdf3e29c41d0 + tags: + - variant-calling + updated: '2014-03-05T18:53:35.283625' +- name: CloudMap Hawaiian and Variant Discovery Mapping on Hawaiian Mapped Samples + (and Variant Calling) workflow _2-7-2014 + owner: gm2123 + steps: 37 + ids: + - - https://usegalaxy.org + - ea817818a6de77e0 + tags: [] + updated: '2014-03-05T18:48:08.216215' +- name: diff & merge of 'tophat & cufflinks' (PE vs Non-PE) + owner: comparor + steps: 9 + ids: + - - https://usegalaxy.org + - eae740bac11ecc91 + tags: + - nascent + - RNA + updated: '2014-02-23T11:11:40.922871' +- name: NGS_SAM + owner: ipopov + steps: 2 + ids: + - 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4ca3b9bb720e9233 + tags: [] + updated: '2014-01-21T23:08:21.397891' +- name: Unnamed workflow + owner: guohuijuan35 + steps: 0 + ids: + - - https://usegalaxy.org + - e73a5cf64bd4a372 + tags: [] + updated: '2014-01-16T08:10:21.289443' +- name: CloudMap Variant Discovery Mapping (Subtracts Crossing Strain from List of + Homozygous and Heterozygous Variants called by GATK Unified Genotyper default + settings)_12-22-2013 + owner: gm2123 + steps: 12 + ids: + - - https://usegalaxy.org + - 65cc7722fb5d626a + tags: [] + updated: '2013-12-21T20:24:16.140883' +- name: CloudMap Variant Discovery Mapping (Subtracts Crossing Strain from List of + Homozygous and Heterozygous Variants called by GATK Unified Genotyper default + settings)_12-21-2013 + owner: gregory-minevich + steps: 12 + ids: + - - https://usegalaxy.org + - 25903aa8a238222d + tags: [] + updated: '2013-12-21T20:03:44.269108' +- name: 'imported: Sort SAM file for Cufflinks' + owner: '' + steps: 5 + ids: + - - https://usegalaxy.org + - b48ff652fc8fbee2 + tags: [] + updated: '2013-12-06T19:17:51.146369' +- name: Differential gene expression for zebrafish RNA-seq + owner: stevetonghk + steps: 15 + ids: + - 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- https://workflowhub.eu + - '46' + tags: + - Climate + - Galaxy + - copernicus + updated: '2023-01-16T13:44:09.000Z' +- name: Climate - Climate 101 + owner: Anne Fouilloux + steps: 13 + ids: + - - https://workflowhub.eu + - '42' + tags: + - Climate + - GTN + updated: '2023-01-16T13:43:36.000Z' +- name: Assembly using Tophat2 and annotation (alternate) + owner: Unknown + steps: 19 + ids: + - - https://workflowhub.eu + - '37' + tags: + - Alignment + - Assembly + - Galaxy + - RNASEQ + - Tophat2 + - covid-19 + updated: '2023-02-13T14:06:46.000Z' +- name: Unicycler assembly and annotation + owner: Unknown + steps: 21 + ids: + - - https://workflowhub.eu + - '38' + tags: + - Alignment + - Annotation + - Assembly + - RNASEQ + - Unicycler + - covid-19 + updated: '2023-02-13T14:06:46.000Z' +- name: StringTie assembly and annotation + owner: Unknown + steps: 22 + ids: + - - https://workflowhub.eu + - '39' + tags: + - Alignment + - Annotation + - Assembly + - RNASEQ + - StringTie + - covid-19 + updated: '2023-02-13T14:06:46.000Z' +- name: Assembly using Tophat2 and annotation + owner: Unknown + steps: 24 + ids: + - - https://workflowhub.eu + - '40' + tags: + - Alignment + - Annotation + - Assembly + - RNASEQ + - Tophat2 + - covid-19 + updated: '2023-02-13T14:06:46.000Z' +- name: 'COVID-19: VARSCAN' + owner: Unknown + steps: 19 + ids: + - - https://workflowhub.eu + - '36' + tags: + - Galaxy + - INDELs + - SNPs + - VARSCAN2 + updated: '2023-02-13T14:06:46.000Z' +- name: 'COVID-19: GATK4' + owner: Unknown + steps: 16 + ids: + - - https://workflowhub.eu + - '35' + tags: + - GATK4 + - Galaxy + - INDELs + - SNPs + updated: '2023-02-13T14:06:46.000Z' +- name: Pathway Ranker + owner: Melchior du Lac + steps: 12 + ids: + - - https://workflowhub.eu + - '25' + tags: + - Retrosynthesis + - Synthetic Biology + - metabolic engineering + - pathway design + - pathway prediction + updated: '2023-01-16T13:41:47.000Z' +- name: RetroSynthesis + owner: Melchior du Lac + steps: 7 + ids: + - - https://workflowhub.eu + - '24' + tags: + - Retrosynthesis + - Synthetic Biology + - metabolic engineering + - pathway design + - pathway prediction + updated: '2023-01-16T13:41:42.000Z' +- name: Genetic Design + owner: Melchior du Lac + steps: 7 + ids: + - - https://workflowhub.eu + - '23' + tags: + - Retrosynthesis + - genetic design + - pathway prediction + updated: '2023-01-16T13:41:35.000Z' +- name: Pathway Analysis + owner: Melchior du Lac + steps: 3 + ids: + - - https://workflowhub.eu + - '22' + tags: + - Retrosynthesis + updated: '2023-01-16T13:41:28.000Z' +- name: Cheminformatics - XChem combined + owner: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, + Jack Scantlebury, Susan Leung, Frank von Delft + steps: 3 + ids: + - - https://workflowhub.eu + - '18' + tags: + - covid-19 + updated: '2023-01-16T13:41:21.000Z' +- name: Cheminformatics - Filter results + owner: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, + Jack Scantlebury, Susan Leung, Frank von Delft + steps: 13 + ids: + - - https://workflowhub.eu + - '17' + tags: + - covid-19 + updated: '2023-01-16T13:41:12.000Z' +- name: Cheminformatics - TransFS scoring + owner: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, + Jack Scantlebury, Susan Leung, Frank von Delft + steps: 3 + ids: + - - https://workflowhub.eu + - '16' + tags: + - covid-19 + updated: '2023-01-16T13:41:04.000Z' +- name: Cheminformatics - SuCOS scoring + owner: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, + Jack Scantlebury, Susan Leung, Frank von Delft + steps: 5 + ids: + - - https://workflowhub.eu + - '15' + tags: + - covid-19 + updated: '2023-01-16T13:40:57.000Z' +- name: Cheminformatics - Docking + owner: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, + Jack Scantlebury, Susan Leung, Frank von Delft + steps: 4 + ids: + - - https://workflowhub.eu + - '14' + tags: + - covid-19 + updated: '2023-01-16T13:40:50.000Z' +- name: Cheminformatics - Active site generation + owner: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, + Jack Scantlebury, Susan Leung, Frank von Delft + steps: 2 + ids: + - - https://workflowhub.eu + - '13' + tags: + - covid-19 + updated: '2023-01-16T13:40:43.000Z' +- name: Cheminformatics - Enumerate ligands for docking + owner: Tim Dudgeon, Simon Bray, Gianmauro Cuccuru, Björn Grüning, Rachael Skyner, + Jack Scantlebury, Susan Leung, Frank von Delft + steps: 4 + ids: + - - https://workflowhub.eu + - '12' + tags: + - covid-19 + updated: '2023-01-16T13:40:34.000Z' +- name: Genomics - Recombination and selection analysis + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 6 + ids: + - - https://workflowhub.eu + - '10' + tags: + - covid-19 + updated: '2023-01-16T13:40:25.000Z' +- name: Genomics - Analysis of S-protein polymorphism + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 3 + ids: + - - https://workflowhub.eu + - '9' + tags: + - covid-19 + updated: '2023-01-16T13:40:19.000Z' +- name: Genomics - SE Variation + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 12 + ids: + - - https://workflowhub.eu + - '8' + tags: + - covid-19 + updated: '2023-01-16T13:40:12.000Z' +- name: Genomics - PE Variation + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 14 + ids: + - - https://workflowhub.eu + - '7' + tags: + - covid-19 + updated: '2023-05-30T12:07:57.000Z' +- name: Genomics - MRCA analysis + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 9 + ids: + - - https://workflowhub.eu + - '6' + tags: + - covid-19 + updated: '2023-01-16T13:39:57.000Z' +- name: Genomics - Assembly of the genome sequence + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 6 + ids: + - - https://workflowhub.eu + - '5' + tags: + - covid-19 + updated: '2023-01-16T13:39:53.000Z' +- name: Genomics - Read pre-processing without downloading from SRA + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 13 + ids: + - - https://workflowhub.eu + - '4' + tags: + - covid-19 + updated: '2023-01-16T13:39:49.000Z' +- name: Genomics - Read pre-processing + owner: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, + Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, + Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei + Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver + steps: 15 + ids: + - - https://workflowhub.eu + - '2' + tags: + - covid-19 + updated: '2023-01-16T13:39:40.000Z' diff --git a/workflows/list.html b/workflows/list.html index 81ef7d1002be05..e00939e2e66311 100644 --- a/workflows/list.html +++ b/workflows/list.html @@ -6,6 +6,11 @@

We are testing a new search experience. Tell us what you think!

+

+This site +currently lists {{ site.data['workflows'] | size }} workflows from +UseGalaxy.org, UseGalaxy.eu, UseGalaxy.org.au, and WorkflowHub.eu. It is updated weekly. +

@@ -53,7 +58,11 @@ {{ workflow.updated }} {% for id in workflow.ids %} + {% if id[0] == "https://workflowhub.eu" %} + {{ id[0] }} + {% else %} {{ id[0] }} + {% endif %} {% endfor %}