Template update for nf-core/tools version 2.6

.github/workflows/awsfulltest.yml

@@ -28,3 +28,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log

.github/workflows/awstest.yml

@@ -23,3 +23,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log

.prettierignore

@@ -1,4 +1,5 @@
 email_template.html
+adaptivecard.json
 .nextflow*
 work/
 data/

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

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/taxprofiler 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") %>
+                                    ]
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        }
+    ]
+}

assets/methods_description_template.yml

@@ -0,0 +1,25 @@
+id: "nf-core-taxprofiler-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "nf-core/taxprofiler Methods Description"
+section_href: "https://github.com/nf-core/taxprofiler"
+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 '${workflow}' object
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using nf-core/taxprofiler v${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>

assets/multiqc_config.yml

@@ -3,9 +3,11 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/taxprofiler" target="_blank">documentation</a>.
 report_section_order:
-  software_versions:
+  "nf-core-taxprofiler-methods-description":
     order: -1000
-  "nf-core-taxprofiler-summary":
+  software_versions:
     order: -1001
+  "nf-core-taxprofiler-summary":
+    order: -1002
 
 export_plots: true

docs/usage.md

@@ -237,6 +237,14 @@ 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.

lib/NfcoreTemplate.groovy

@@ -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
     //

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" +
                 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         }
     }

lib/WorkflowTaxprofiler.groovy

@@ -2,6 +2,8 @@
 // This file holds several functions specific to the workflow/taxprofiler.nf in the nf-core/taxprofiler pipeline
 //
 
+import groovy.text.SimpleTemplateEngine
+
 class WorkflowTaxprofiler {
 
     //
@@ -42,6 +44,23 @@ class WorkflowTaxprofiler {
         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
     //

main.nf

@@ -4,7 +4,8 @@
     nf-core/taxprofiler
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/nf-core/taxprofiler
-Website: https://nf-co.re/taxprofiler
+
+    Website: https://nf-co.re/taxprofiler
     Slack  : https://nfcore.slack.com/channels/taxprofiler
 ----------------------------------------------------------------------------------------
 */

modules.json

@@ -2,20 +2,21 @@
     "name": "nf-core/taxprofiler",
     "homePage": "https://github.com/nf-core/taxprofiler",
     "repos": {
-        "nf-core/modules": {
-            "git_url": "https://github.com/nf-core/modules.git",
+        "https://github.com/nf-core/modules.git": {
             "modules": {
-                "custom/dumpsoftwareversions": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
-                },
-                "fastqc": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
-                },
-                "multiqc": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
+                "nf-core": {
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    }
                 }
             }
         }

modules/nf-core/custom/dumpsoftwareversions/main.nf

@@ -1,11 +1,11 @@
 process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_low'
+    label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path versions

modules/nf-core/fastqc/main.nf

@@ -44,4 +44,16 @@ process FASTQC {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    touch ${prefix}.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/multiqc/main.nf

@@ -1,31 +0,0 @@
-process MULTIQC {
-    label 'process_medium'
-
-    conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
-
-    input:
-    path multiqc_files
-
-    output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    """
-    multiqc -f $args .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
-    """
-}

modules/nf-core/multiqc/main.nf

@@ -0,0 +1,53 @@
+process MULTIQC {
+    label 'process_single'
+
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+
+    input:
+    path  multiqc_files, stageAs: "?/*"
+    path(multiqc_config)
+    path(extra_multiqc_config)
+    path(multiqc_logo)
+
+    output:
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
+    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    """
+    multiqc \\
+        --force \\
+        $args \\
+        $config \\
+        $extra_config \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+}

modules/nf-core/multiqc/meta.yml

@@ -12,11 +12,25 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+
 input:
   - multiqc_files:
       type: file
       description: |
         List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+
 output:
   - report:
       type: file
@@ -38,3 +52,4 @@ authors:
   - "@abhi18av"
   - "@bunop"
   - "@drpatelh"
+  - "@jfy133"

nextflow.config

@@ -21,7 +21,9 @@ params {
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
+    multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
+    multiqc_methods_description = null
 
     // Boilerplate options
     outdir                     = null
@@ -31,6 +33,7 @@ params {
     email_on_fail              = null
     plaintext_email            = false
     monochrome_logs            = false
+    hook_url                   = null
     help                       = false
     validate_params            = true
     show_hidden_params         = false
@@ -74,7 +77,6 @@ try {
 // }
 
 
-
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
@@ -189,6 +191,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
     version         = '1.0dev'
+    doi             = ''
 }
 
 // Load modules.config for DSL2 module specific options

nextflow_schema.json

@@ -213,12 +213,30 @@
                     "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.",

workflows/taxprofiler.nf

@@ -23,8 +23,10 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-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)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -46,9 +48,9 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { FASTQC                      } from '../modules/nf-core/modules/fastqc/main'
-include { MULTIQC                     } from '../modules/nf-core/modules/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
+include { FASTQC                      } from '../modules/nf-core/fastqc/main'
+include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -89,15 +91,20 @@ workflow TAXPROFILER {
     workflow_summary    = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
     ch_workflow_summary = Channel.value(workflow_summary)
 
+    methods_description    = WorkflowTaxprofiler.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
+    ch_methods_description = Channel.value(methods_description)
+
     ch_multiqc_files = Channel.empty()
-    ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
 
     MULTIQC (
-        ch_multiqc_files.collect()
+        ch_multiqc_files.collect(),
+        ch_multiqc_config.collect().ifEmpty([]),
+        ch_multiqc_custom_config.collect().ifEmpty([]),
+        ch_multiqc_logo.collect().ifEmpty([])
     )
     multiqc_report = MULTIQC.out.report.toList()
     ch_versions    = ch_versions.mix(MULTIQC.out.versions)
@@ -114,6 +121,9 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
     }
     NfcoreTemplate.summary(workflow, params, log)
+    if (params.hook_url) {
+        NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log)
+    }
 }
 
 /*