Merge pull request #880 from nf-core/nf-core-template-merge-2.6

drpatelh · web-flow · commit 2a32479992ed · 2022-10-09T11:45:44.000+01:00
Important! Template update for nf-core/tools v2.6
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -30,3 +30,7 @@ jobs:
               "aligner": "${{ matrix.aligner }}"
             }
           profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -23,3 +23,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/CITATION.cff b/CITATION.cff
@@ -13,8 +13,8 @@ authors:
     given-names: Johannes
   - family-names: Wilm
     given-names: Andreas
-  - family-names: Ulysse Garcia
-    given-names: Maxime
+  - family-names: Garcia
+    given-names: Maxime Ulysse
   - family-names: Di Tommaso
     given-names: Paolo
   - family-names: Nahnsen
@@ -39,8 +39,8 @@ prefered-citation:
       given-names: Johannes
     - family-names: Wilm
       given-names: Andreas
-    - family-names: Ulysse Garcia
-      given-names: Maxime
+    - family-names: Garcia
+      given-names: Maxime Ulysse
     - family-names: Di Tommaso
       given-names: Paolo
     - family-names: Nahnsen
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
@@ -0,0 +1,67 @@
+{
+    "type": "message",
+    "attachments": [
+        {
+            "contentType": "application/vnd.microsoft.card.adaptive",
+            "contentUrl": null,
+            "content": {
+                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                "msteams": {
+                    "width": "Full"
+                },
+                "type": "AdaptiveCard",
+                "version": "1.2",
+                "body": [
+                    {
+                        "type": "TextBlock",
+                        "size": "Large",
+                        "weight": "Bolder",
+                        "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
+                        "text": "nf-core/rnaseq v${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") %>
+                                    ]
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        }
+    ]
+}
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
@@ -0,0 +1,25 @@
+id: "nf-core-rnaseq-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "nf-core/rnaseq Methods Description"
+section_href: "https://github.com/nf-core/rnaseq"
+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 '${workflow}' object
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using nf-core/rnaseq v${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>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -3,10 +3,12 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/rnaseq" target="_blank">documentation</a>.
 report_section_order:
-  software_versions:
+  "nf-core-rnaseq-methods-description":
     order: -1000
-  nf-core-rnaseq-summary:
+  software_versions:
     order: -1001
+  "nf-core-rnaseq-summary":
+    order: -1002
 
 export_plots: true
 
diff --git a/docs/usage.md b/docs/usage.md
@@ -296,6 +296,14 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
+## Azure Resource Requests
+
+To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
+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 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).
+
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
@@ -150,6 +150,61 @@ 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
     //
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -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" +
                 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         }
     }
diff --git a/lib/WorkflowRnaseq.groovy b/lib/WorkflowRnaseq.groovy
@@ -2,6 +2,8 @@
 // This file holds several functions specific to the workflow/rnaseq.nf in the nf-core/rnaseq pipeline
 //
 
+import groovy.text.SimpleTemplateEngine
+
 class WorkflowRnaseq {
 
     //
@@ -250,6 +252,23 @@ class WorkflowRnaseq {
         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}\'>${meta.manifest_map.doi}</a>)" : ""
+        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+        def methods_text = mqc_methods_yaml.text
+
+        def engine =  new SimpleTemplateEngine()
+        def description_html = engine.createTemplate(methods_text).make(meta)
+
+        return description_html
     }//
     // Exit pipeline if incorrect --genome key provided
     //
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -11,6 +11,8 @@ process MULTIQC {
     path multiqc_custom_config
     path software_versions
     path workflow_summary
+    path methods_description
+    path logo
     path fail_trimming_summary
     path fail_mapping_summary
     path fail_strand_check
diff --git a/nextflow.config b/nextflow.config
@@ -91,11 +91,14 @@ params {
     outdir                     = null
     multiqc_config             = null
     multiqc_title              = null
+    multiqc_logo               = null
+    multiqc_methods_description = null
     email                      = null
     email_on_fail              = null
     max_multiqc_email_size     = '25.MB'
     plaintext_email            = false
     monochrome_logs            = false
+    hook_url                   = null
     help                       = false
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     tracedir                   = "${params.outdir}/pipeline_info"
@@ -247,6 +250,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
     version         = '3.10dev'
+    doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 
 // Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -658,12 +658,30 @@
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
+                "hook_url": {
+                    "type": "string",
+                    "description": "Incoming hook URL for messaging service",
+                    "fa_icon": "fas fa-people-group",
+                    "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.",
+                    "hidden": true
+                },
                 "multiqc_config": {
                     "type": "string",
                     "description": "Custom config file to supply to MultiQC.",
                     "fa_icon": "fas fa-cog",
                     "hidden": true
                 },
+                "multiqc_logo": {
+                    "type": "string",
+                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
+                    "fa_icon": "fas fa-image",
+                    "hidden": true
+                },
+                "multiqc_methods_description": {
+                    "type": "string",
+                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
+                    "fa_icon": "fas fa-cog"
+                },
                 "tracedir": {
                     "type": "string",
                     "description": "Directory to keep pipeline Nextflow logs and reports.",
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
@@ -80,8 +80,10 @@ if (params.fasta && params.gtf) {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
+ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
+ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
 
 // Header files for MultiQC
 ch_pca_header_multiqc        = file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true)
@@ -763,11 +765,16 @@ workflow RNASEQ {
         workflow_summary    = WorkflowRnaseq.paramsSummaryMultiqc(workflow, summary_params)
         ch_workflow_summary = Channel.value(workflow_summary)
 
+        methods_description    = WorkflowRnaseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
+        ch_methods_description = Channel.value(methods_description)
+    
         MULTIQC (
             ch_multiqc_config,
             ch_multiqc_custom_config.collect().ifEmpty([]),
             CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
             ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'),
+            ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'),
+            ch_multiqc_logo.collect().ifEmpty([]),
             ch_fail_trimming_multiqc.ifEmpty([]),
             ch_fail_mapping_multiqc.ifEmpty([]),
             ch_fail_strand_multiqc.ifEmpty([]),
@@ -814,6 +821,11 @@ workflow.onComplete {
     if (params.email || params.email_on_fail) {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report, fail_percent_mapped)
     }
+
+    if (params.hook_url) {
+        NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log)
+    }
+
     NfcoreTemplate.summary(workflow, params, log, fail_percent_mapped, pass_percent_mapped)
 }
 

Original file line number	Diff line number	Diff line change
`@@ -30,3 +30,7 @@ jobs:`
`30`	`30`	`"aligner": "${{ matrix.aligner }}"`
`31`	`31`	`}`
`32`	`32`	`profiles: test_full,aws_tower`
	`33`	`+ - uses: actions/upload-artifact@v3`
	`34`	`+ with:`
	`35`	`+ name: Tower debug log file`
	`36`	`+ path: tower_action_*.log`
Original file line number	Diff line number	Diff line change
`@@ -23,3 +23,7 @@ jobs:`
`23`	`23`	`"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-test-${{ github.sha }}"`
`24`	`24`	`}`
`25`	`25`	`profiles: test,aws_tower`
	`26`	`+ - uses: actions/upload-artifact@v3`
	`27`	`+ with:`
	`28`	`+ name: Tower debug log file`
	`29`	`+ path: tower_action_*.log`