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Update API documentation
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‎src/main/resources/templates/apidocs.html‎

Lines changed: 174 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -59,14 +59,31 @@ <h4>Parameters</h4>
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<tr>
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<td>url</td>
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<td>String</td>
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<td>The Github URL to the workflow</td>
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<td>The URL of the repository. Either a Gitlab or Github URL, or any Git repository URL.</td>
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</tr>
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<tr>
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<td>branch</td>
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<td>String</td>
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<td>The branch of the repository. Required if the URL is not from Gitlab or Github.</td>
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</tr>
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<tr>
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<td>path</td>
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<td>String</td>
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<td>The path within the repository to the workflow file. Required if the URL is not from Gitlab or Github.</td>
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</tr>
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</table>
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<h4>Input</h4>
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<pre class="highlight json">
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{
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"url": "https://github.com/common-workflow-language/workflows/tree/master/workflows/compile/compile1.cwl"
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}
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</pre>
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<pre class="highlight json">
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{
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"url": "https://bitbucket.org/markrobinson96/workflows.git",
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"branch": "master",
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"path": "/workflows/make-to-cwl/dna.cwl"
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}
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</pre>
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<h4>Success</h4>
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<pre>
@@ -84,7 +101,7 @@ <h4>Error</h4>
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<h3 id="workflowDetails">Get Workflow Details</h3>
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<span class="method get">GET</span>
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<pre>/workflows/:githubURL</pre>
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<pre>/workflows/:url</pre>
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<h4>Parameters</h4>
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<table class="table">
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<tr>
@@ -93,9 +110,9 @@ <h4>Parameters</h4>
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<th>Description</th>
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</tr>
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<tr>
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<td>githubURL</td>
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<td>url</td>
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<td>String</td>
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<td>Partial github URL to the workflow (no "https://")</td>
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<td>Partial URL to the workflow eg "github.com/owner/repo/tree/branch/workflow.cwl" or "bitbucket.org/owner/repo.git/master/workflow.cwl</td>
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</tr>
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</table>
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<h4>Success 200</h4>
@@ -106,14 +123,9 @@ <h4>Success 200</h4>
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<th>Description</th>
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</tr>
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<tr>
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<td>retrievedFrom.owner</td>
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<td>retrievedFrom.repoUrl</td>
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<td>String</td>
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<td>Github username or organisation name</td>
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</tr>
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<tr>
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<td>retrievedFrom.repoName</td>
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<td>String</td>
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<td>Github repository name</td>
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<td>URL of the Github repository</td>
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</tr>
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<tr>
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<td>retrievedFrom.branch</td>
@@ -128,7 +140,17 @@ <h4>Success 200</h4>
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<tr>
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<td>retrievedFrom.url</td>
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<td>URL</td>
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<td>The full Github URL to the workflow</td>
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<td>The URL to the page on the site if type is not GENERIC, otherwise the same as repoUrl</td>
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</tr>
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<tr>
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<td>retrievedFrom.rawUrl</td>
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<td>URL</td>
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<td>The URL directly to the file if type is not GENERIC, otherwise the same as repoUrl</td>
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</tr>
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<tr>
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<td>retrievedFrom.type</td>
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<td>Enum</td>
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<td>One of GENERIC, GITHUB, GITLAB, BITBUCKET</td>
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</tr>
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<tr>
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<td>retrievedOn</td>
@@ -140,6 +162,11 @@ <h4>Success 200</h4>
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<td>String</td>
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<td>The last commit ID on the branch</td>
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</tr>
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<tr>
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<td>packedWorkflowID</td>
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<td>String</td>
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<td>The ID of the workflow within the file, if this is a packed CWL file (contains a <a href="http://www.commonwl.org/draft-3/SchemaSalad.html#Document_graph">document graph</a>).</td>
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</tr>
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<tr>
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<td>label</td>
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<td>String</td>
@@ -207,46 +234,39 @@ <h5>Example Response</h5>
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<pre class="highlight json">
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{
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"retrievedFrom": {
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"owner": "common-workflow-language",
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"repoName": "workflows",
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"repoUrl": "https://github.com/common-workflow-language/workflows.git",
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"branch": "master",
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"path": "workflows/lobSTR/lobSTR-workflow.cwl",
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"url": "https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl"
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"url": "https://github.com/common-workflow-language/workflows/blob/master/workflows/lobSTR/lobSTR-workflow.cwl",
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"rawUrl": "https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/lobSTR/lobSTR-workflow.cwl",
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"type": "GITHUB"
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},
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"retrievedOn": 1499175275743,
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"lastCommit": "920c6be45f08e979e715a0018f22c532b024074f",
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"retrievedOn": 1502714218616,
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"lastCommit": "17b65ea19d81527090fded62ffa0e1ba3b25d561",
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"label": "lobSTR-workflow.cwl",
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"inputs": {
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"reference": {
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"doc": "lobSTR's bwa reference files",
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"type": "File"
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},
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"rg-sample": {
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"doc": "Use this in the read group SM tag",
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"type": "String"
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},
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"p1": {
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"doc": "list of files containing the first end of paired end reads in fasta or fastq format",
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"type": "11a1d32ade317199b68e62aa6ce50b3e"
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"type": "ee54066e73d068edfbf9ca5059e14acd"
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},
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"p2": {
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"doc": "list of files containing the second end of paired end reads in fasta or fastq format",
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"type": "f9505470accbbaf6b9e15db2123490aa"
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"type": "79ab371b6d0fdbadbf9a4a89ef393353"
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},
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"output_prefix": {
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"doc": "prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats",
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"type": "String"
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},
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"rg-lib": {
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"doc": "Use this in the read group LB tag",
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"type": "String"
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},
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"strinfo": {
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"doc": "File containing statistics for each STR.",
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"type": "File"
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},
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"noise_model": {
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"doc": "File to read noise model parameters from (.stepmodel)",
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"type": "File"
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}
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},
@@ -266,34 +286,145 @@ <h5>Example Response</h5>
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},
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"steps": {
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"allelotype": {
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"doc": "Run lobSTR allelotype classifier.",
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"run": "allelotype.cwl",
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"runType": "COMMANDLINETOOL"
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"runType": "COMMANDLINETOOL",
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"sources": {
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#allelotype/bam": {
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"sourceID": [
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"samindex"
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],
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"sourceIDs": [
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"samindex"
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]
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},
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"allelotype": {
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"sourceID": [
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"strinfo"
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],
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"sourceIDs": [
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"strinfo"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#allelotype/noise_model": {
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"sourceID": [
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"noise_model"
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],
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"sourceIDs": [
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"noise_model"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#allelotype/reference": {
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"sourceID": [
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"reference"
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],
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"sourceIDs": [
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"reference"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#allelotype/output_prefix": {
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"sourceID": [
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"output_prefix"
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],
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"sourceIDs": [
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"output_prefix"
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]
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}
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}
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},
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"samsort": {
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"doc": "Invoke 'samtools sort' (samtools 1.19)",
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"run": "samtools-sort.cwl",
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"runType": "COMMANDLINETOOL"
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"runType": "COMMANDLINETOOL",
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"sources": {
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"samsort": {
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"sourceID": [
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"lobSTR"
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],
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"sourceIDs": [
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"lobSTR"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#samsort/output_name": {
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"defaultVal": "\\\"aligned.sorted.bam\\\""
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}
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}
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},
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"lobSTR": {
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"label": "lobSTR",
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"doc": "lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.",
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"run": "lobSTR-tool.cwl",
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"runType": "COMMANDLINETOOL"
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"runType": "COMMANDLINETOOL",
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"sources": {
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"lobSTR": {
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"sourceID": [
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"rg-lib"
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],
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"sourceIDs": [
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"rg-lib"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR/p1": {
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"sourceID": [
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"p1"
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],
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"sourceIDs": [
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"p1"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR/p2": {
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"sourceID": [
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"p2"
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],
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"sourceIDs": [
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"p2"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR/output_prefix": {
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"sourceID": [
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"output_prefix"
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],
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"sourceIDs": [
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"output_prefix"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR/rg-sample": {
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"sourceID": [
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"rg-sample"
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],
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"sourceIDs": [
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"rg-sample"
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]
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},
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"file:///data/git/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR/reference": {
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"sourceID": [
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"reference"
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],
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"sourceIDs": [
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"reference"
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]
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}
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}
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},
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"samindex": {
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"doc": "Invoke 'samtools index' to create a 'BAI' index (samtools 1.19)",
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"run": "samtools-index.cwl",
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"runType": "COMMANDLINETOOL"
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"runType": "COMMANDLINETOOL",
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"sources": {
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"samindex": {
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"sourceID": [
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"samsort"
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],
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"sourceIDs": [
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"samsort"
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]
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}
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}
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}
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},
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"dockerLink": "true",
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"cwltoolVersion": " 1.0.20170622090721",
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"visualisationDot": "digraph workflow {\n graph [\n bgcolor = \"#eeeeee\"\n color = \"black\"\n fontsize = \"10\"\n labeljust = \"left\"\n clusterrank = \"local\"\n ranksep = \"0.22\"\n nodesep = \"0.05\"\n ]\n node [\n fontname = \"Helvetica\"\n fontsize = \"10\"\n fontcolor = \"black\"\n shape = \"record\"\n height = \"0\"\n width = \"0\"\n color = \"black\"\n fillcolor = \"lightgoldenrodyellow\"\n style = \"filled\"\n ];\n edge [\n fontname=\"Helvetica\"\n fontsize=\"8\"\n fontcolor=\"black\"\n color=\"black\"\n arrowsize=\"0.7\"\n ];\n subgraph cluster_inputs {\n rank = \"same\";\n style = \"dashed\";\n label = \"Workflow Inputs\";\n \"lobSTR-workflow.cwl#output_prefix\" [fillcolor=\"#94DDF4\",label=\"output_prefix\"];\n \"lobSTR-workflow.cwl#reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n \"lobSTR-workflow.cwl#p2\" [fillcolor=\"#94DDF4\",label=\"p2\"];\n \"lobSTR-workflow.cwl#p2\" [fillcolor=\"#94DDF4\",label=\"p2\"];\n \"lobSTR-workflow.cwl#strinfo\" [fillcolor=\"#94DDF4\",label=\"strinfo\"];\n \"lobSTR-workflow.cwl#p1\" [fillcolor=\"#94DDF4\",label=\"p1\"];\n \"lobSTR-workflow.cwl#p1\" [fillcolor=\"#94DDF4\",label=\"p1\"];\n \"lobSTR-workflow.cwl#rg-lib\" [fillcolor=\"#94DDF4\",label=\"rg-lib\"];\n \"lobSTR-workflow.cwl#noise_model\" [fillcolor=\"#94DDF4\",label=\"noise_model\"];\n \"lobSTR-workflow.cwl#rg-sample\" [fillcolor=\"#94DDF4\",label=\"rg-sample\"];\n }\n subgraph cluster_outputs {\n rank = \"same\";\n style = \"dashed\";\n label = \"Workflow Outputs\";\n \"lobSTR-workflow.cwl#bam_stats\" [fillcolor=\"#94DDF4\",label=\"bam_stats\"];\n \"lobSTR-workflow.cwl#vcf_stats\" [fillcolor=\"#94DDF4\",label=\"vcf_stats\"];\n \"lobSTR-workflow.cwl#vcf\" [fillcolor=\"#94DDF4\",label=\"vcf\"];\n \"lobSTR-workflow.cwl#bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n }\n \"lobSTR-workflow.cwl#allelotype\" [label=\"allelotype\"];\n \"lobSTR-workflow.cwl#samindex\" [label=\"samindex\"];\n \"lobSTR-workflow.cwl#samsort\" [label=\"samsort\"];\n \"lobSTR-workflow.cwl#lobSTR\" [label=\"lobSTR\"];\n}\n",
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"robundle": "/robundle/github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl",
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"visualisationXdot": "/graph/xdot/github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl",
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"visualisationPng": "/graph/png/github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl",
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"visualisationSvg": "/graph/svg/github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl"
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"dockerLink": "https://hub.docker.com/r/rabix/lobstr",
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"cwltoolVersion": "1.0.20170810192106",
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"visualisationDot": "digraph workflow {\n graph [\n bgcolor = \"#eeeeee\"\n color = \"black\"\n fontsize = \"10\"\n labeljust = \"left\"\n clusterrank = \"local\"\n ranksep = \"0.22\"\n nodesep = \"0.05\"\n ]\n node [\n fontname = \"Helvetica\"\n fontsize = \"10\"\n fontcolor = \"black\"\n shape = \"record\"\n height = \"0\"\n width = \"0\"\n color = \"black\"\n fillcolor = \"lightgoldenrodyellow\"\n style = \"filled\"\n ];\n edge [\n fontname=\"Helvetica\"\n fontsize=\"8\"\n fontcolor=\"black\"\n color=\"black\"\n arrowsize=\"0.7\"\n ];\n subgraph cluster_inputs {\n rank = \"same\";\n style = \"dashed\";\n label = \"Workflow Inputs\";\n \"p2\" [fillcolor=\"#94DDF4\",label=\"p2\"];\n \"p2\" [fillcolor=\"#94DDF4\",label=\"p2\"];\n \"output_prefix\" [fillcolor=\"#94DDF4\",label=\"output_prefix\"];\n \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n \"noise_model\" [fillcolor=\"#94DDF4\",label=\"noise_model\"];\n \"strinfo\" [fillcolor=\"#94DDF4\",label=\"strinfo\"];\n \"p1\" [fillcolor=\"#94DDF4\",label=\"p1\"];\n \"p1\" [fillcolor=\"#94DDF4\",label=\"p1\"];\n \"rg-lib\" [fillcolor=\"#94DDF4\",label=\"rg-lib\"];\n \"rg-sample\" [fillcolor=\"#94DDF4\",label=\"rg-sample\"];\n }\n subgraph cluster_outputs {\n rank = \"same\";\n style = \"dashed\";\n labelloc = \"b\";\n label = \"Workflow Outputs\";\n \"bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n \"vcf\" [fillcolor=\"#94DDF4\",label=\"vcf\"];\n \"bam_stats\" [fillcolor=\"#94DDF4\",label=\"bam_stats\"];\n \"vcf_stats\" [fillcolor=\"#94DDF4\",label=\"vcf_stats\"];\n }\n \"allelotype\" [label=\"allelotype\"];\n \"samsort\" [label=\"samsort\"];\n \"lobSTR\" [label=\"lobSTR\"];\n \"samindex\" [label=\"samindex\"];\n \"strinfo\" -> \"allelotype\" [label=\"strinfo\"];\n \"reference\" -> \"allelotype\" [label=\"reference\"];\n \"output_prefix\" -> \"allelotype\" [label=\"output_prefix\"];\n \"noise_model\" -> \"allelotype\" [label=\"noise_model\"];\n \"samindex\" -> \"allelotype\" [label=\"bam\"];\n \"lobSTR\" -> \"samsort\" [label=\"input\"];\n \"default1\" -> \"samsort\" [label=\"output_name\"];\n \"default1\" [label=\"\\\"aligned.sorted.bam\\\"\", fillcolor=\"#D5AEFC\"];\n \"rg-lib\" -> \"lobSTR\" [label=\"rg-lib\"];\n \"rg-sample\" -> \"lobSTR\" [label=\"rg-sample\"];\n \"p2\" -> \"lobSTR\" [label=\"p2\"];\n \"p1\" -> \"lobSTR\" [label=\"p1\"];\n \"reference\" -> \"lobSTR\" [label=\"reference\"];\n \"output_prefix\" -> \"lobSTR\" [label=\"output_prefix\"];\n \"samsort\" -> \"samindex\" [label=\"input\"];\n \"samindex\" -> \"bam\";\n \"allelotype\" -> \"vcf\";\n \"lobSTR\" -> \"bam_stats\";\n \"allelotype\" -> \"vcf_stats\";\n}\n",
424+
"visualisationPng": "/graph/png/github.com/common-workflow-language/workflows/blob/master/workflows/lobSTR/lobSTR-workflow.cwl",
425+
"visualisationSvg": "/graph/svg/github.com/common-workflow-language/workflows/blob/master/workflows/lobSTR/lobSTR-workflow.cwl",
426+
"roBundle": "/robundle/github.com/common-workflow-language/workflows/blob/master/workflows/lobSTR/lobSTR-workflow.cwl",
427+
"visualisationXdot": "/graph/xdot/github.com/common-workflow-language/workflows/blob/master/workflows/lobSTR/lobSTR-workflow.cwl"
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}
298429
</pre>
299430

@@ -454,7 +585,7 @@ <h5>Example Responses</h5>
454585
<h4>Finished 303</h4>
455586
<pre>
456587
HTTP/1.1 303 See Other
457-
Location: /workflows/:githubURL
588+
Location: /workflows/:url
458589
</pre>
459590

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<h2>Examples</h2>

‎src/main/resources/templates/index.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,7 @@ <h2>Workflow URL</h2>
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<strong>Don't know what to view?</strong> Try these from <i>common-workflow-language/workflows</i>:
5454
<a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/compile/compile1.cwl">compile</a>,
5555
<a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/make-to-cwl/dna.cwl">make-to-cwl</a>,
56-
<a class="example" href="https://github.com/common-workflow-language/workflows/tree/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl">lobSTR</a>
56+
<a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl">lobSTR</a>
5757
or <a href="/workflows">explore the collection</a>
5858
</div>
5959
<form id="add" action="#" th:action="@{/workflows}" th:object="${workflowForm}" method="POST">

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