nf-core · maxulysse · Oct 5, 2022 · Oct 4, 2022 · Oct 5, 2022 · Oct 5, 2022
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -26,3 +26,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test"
             }
           profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -23,3 +23,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
@@ -1,4 +1,5 @@
 email_template.html
+adaptivecard.json
 .nextflow*
 work/
 data/

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#762](https://github.com/nf-core/sarek/pull/762) - Back to dev
 - [#762](https://github.com/nf-core/sarek/pull/762) - Update deepvariant module
+- [#773](https://github.com/nf-core/sarek/pull/773) - Sync `TEMPLATE` with `tools` `2.6`
 
 ### Fixed
 

@@ -0,0 +1,67 @@
+{
+    "type": "message",
+    "attachments": [
+        {
+            "contentType": "application/vnd.microsoft.card.adaptive",
+            "contentUrl": null,
+            "content": {
+                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                "msteams": {
+                    "width": "Full"
+                },
+                "type": "AdaptiveCard",
+                "version": "1.2",
+                "body": [
+                    {
+                        "type": "TextBlock",
+                        "size": "Large",
+                        "weight": "Bolder",
+                        "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
+                        "text": "nf-core/sarek v${version} - ${runName}",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "spacing": "None",
+                        "text": "Completed at ${dateComplete} (duration: ${duration})",
+                        "isSubtle": true,
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "The command used to launch the workflow was as follows:",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "${commandLine}",
+                        "isSubtle": true,
+                        "wrap": true
+                    }
+                ],
+                "actions": [
+                    {
+                        "type": "Action.ShowCard",
+                        "title": "Pipeline Configuration",
+                        "card": {
+                            "type": "AdaptiveCard",
+                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                            "body": [
+                                {
+                                    "type": "FactSet",
+                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
+                                    ]
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        }
+    ]
+}
@@ -0,0 +1,25 @@
+id: "nf-core-sarek-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "nf-core/sarek Methods Description"
+section_href: "https://github.com/nf-core/sarek"
+plot_type: "html"
+## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## You inject any metadata in the Nextflow '${workflow}' object
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using nf-core/sarek v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
+  <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
+  <pre><code>${workflow.commandLine}</code></pre>
+  <h4>References</h4>
+  <ul>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+  </ul>
+  <div class="alert alert-info">
+    <h5>Notes:</h5>
+    <ul>
+      ${nodoi_text}
+      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+    </ul>
+  </div>
@@ -7,10 +7,12 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/sarek" target="_blank">documentation</a>.
 report_section_order:
-  software_versions:
+  "nf-core-sarek-methods-description":
     order: -1000
-  nf-core-sarek-summary:
+  software_versions:
     order: -1001
+  "nf-core-sarek-summary":
+    order: -1002
 
 export_plots: true
 

@@ -473,7 +473,7 @@ If you have any questions or issues please send us a message on [Slack](https://
 ## Azure Resource Requests
 
 To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recomend providing a compute `params.vm_type` of `Standard_E64_v3` VMs by default but these options can be changed if required.
+We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
 
 Note that the choice of VM size depends on your
F438
 quota and the overall workload during the analysis.
 For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).

@@ -145,6 +145,61 @@ class NfcoreTemplate {
         output_tf.withWriter { w -> w << email_txt }
     }
 
+    //
+    // Construct and send adaptive card
+    // https://adaptivecards.io
+    //
+    public static void adaptivecard(workflow, params, summary_params, projectDir, log) {
+        def hook_url = params.hook_url
+
+        def summary = [:]
+        for (group in summary_params.keySet()) {
+            summary << summary_params[group]
+        }
+
+        def misc_fields = [:]
+        misc_fields['start']                                = workflow.start
+        misc_fields['complete']                             = workflow.complete
+        misc_fields['scriptfile']                           = workflow.scriptFile
+        misc_fields['scriptid']                             = workflow.scriptId
+        if (workflow.repository) misc_fields['repository']  = workflow.repository
+        if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+        if (workflow.revision)   misc_fields['revision']    = workflow.revision
+        misc_fields['nxf_version']                          = workflow.nextflow.version
+        misc_fields['nxf_build']                            = workflow.nextflow.build
+        misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+        def msg_fields = [:]
+        msg_fields['version']      = workflow.manifest.version
+        msg_fields['runName']      = workflow.runName
+        msg_fields['success']      = workflow.success
+        msg_fields['dateComplete'] = workflow.complete
+        msg_fields['duration']     = workflow.duration
+        msg_fields['exitStatus']   = workflow.exitStatus
+        msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+        msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+        msg_fields['commandLine']  = workflow.commandLine
+        msg_fields['projectDir']   = workflow.projectDir
+        msg_fields['summary']      = summary << misc_fields
+
+        // Render the JSON template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        def hf = new File("$projectDir/assets/adaptivecard.json")
+        def json_template = engine.createTemplate(hf).make(msg_fields)
+        def json_message  = json_template.toString()
+
+        // POST
+        def post = new URL(hook_url).openConnection();
+        post.setRequestMethod("POST")
+        post.setDoOutput(true)
+        post.setRequestProperty("Content-Type", "application/json")
+        post.getOutputStream().write(json_message.getBytes("UTF-8"));
+        def postRC = post.getResponseCode();
+        if (! postRC.equals(200)) {
+            log.warn(post.getErrorStream().getText());
+        }
+    }
+
     //
     // Print pipeline summary on completion
     //

@@ -21,19 +21,26 @@ class Utils {
         }
 
         // Check that all channels are present
-        def required_channels = ['conda-forge', 'bioconda', 'defaults']
-        def conda_check_failed = !required_channels.every { ch -> ch in channels }
+        // This channel list is ordered by required channel priority.
+        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+        def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
         // Check that they are in the right order
-        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
-        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+        def channel_priority_violation = false
+        def n = required_channels_in_order.size()
+        for (int i = 0; i < n - 1; i++) {
+            channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+        }
 
-        if (conda_check_failed) {
+        if (channels_missing | channel_priority_violation) {
             log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                 "  There is a problem with your Conda configuration!\n\n" +
                 "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-                "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
-                "  NB: The order of the channels matters!\n" +
+                "  Please refer to https://bioconda.github.io/\n" +
+                "  The observed channel order is \n" +
+                "  ${channels}\n" +
+                "  but the following channel order is required:\n" +
+                "  ${required_channels_in_order}\n" +
                 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         }
     }

@@ -2,6 +2,8 @@
 // This file holds several functions specific to the workflow/sarek.nf in the nf-core/sarek pipeline
 //
 
+import groovy.text.SimpleTemplateEngine
+
 class WorkflowSarek {
 
     //
@@ -42,6 +44,23 @@ class WorkflowSarek {
         yaml_file_text        += "data: |\n"
         yaml_file_text        += "${summary_section}"
         return yaml_file_text
+    }
+
+    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
+        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+        def meta = [:]
+        meta.workflow = run_workflow.toMap()
+        meta["manifest_map"] = run_workflow.manifest.toMap()
+
+        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
+        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+        def methods_text = mqc_methods_yaml.text
+
+        def engine =  new SimpleTemplateEngine()
+        def description_html = engine.createTemplate(methods_text).make(meta)
+
+        return description_html
     }//
     // Exit pipeline if incorrect --genome key provided
     //

@@ -144,8 +144,7 @@
                     },
                     "gatk4/cnnscorevariants": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "patch": "modules/nf-core/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff"
+                        "git_sha": "1832dc139342122c9617bfcd5c38c8fb8dd060ad"
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",

@@ -86,9 +86,11 @@ params {
     vep_include_fasta   = false // Don't use fasta file for annotation with VEP
 
     // MultiQC options
-    multiqc_config         = null
-    multiqc_title          = null
-    max_multiqc_email_size = '25.MB'
+    multiqc_config             = null
+    multiqc_title              = null
+    multiqc_logo               = null
+    max_multiqc_email_size     = '25.MB'
+    multiqc_methods_description = null
 
     // Boilerplate options
     outdir                     = 'results'
@@ -98,6 +100,7 @@ params {
     email_on_fail              = null
     plaintext_email            = false
     monochrome_logs            = false
+    hook_url                   = null
     help                       = false
     validate_params            = true
     show_hidden_params         = false
@@ -278,6 +281,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
     version         = '3.1dev'
+    doi             = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683'
 }
 
 // Load modules.config for DSL2 module specific options