Merge pull request #138 from nf-core/nf-core-template-merge-2.6

Important! Template update for nf-core/tools v2.6

.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
+  - family-names: Garcia
-    given-names: Maxime
+    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
+    - family-names: Garcia
-      given-names: Maxime
+      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

@@ -3,10 +3,12 @@ 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

@@ -400,6 +400,14 @@ 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']
+        // This channel list is ordered by required channel priority.
-        def conda_check_failed = !required_channels.every { ch -> ch in channels }
+        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'))
+        def channel_priority_violation = false
-        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+        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" +
+                "  Please refer to https://bioconda.github.io/\n" +
-                "  NB: The order of the channels matters!\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

@@ -4,6 +4,7 @@
     nf-core/taxprofiler
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/nf-core/taxprofiler
+
     Website: https://nf-co.re/taxprofiler
     Slack  : https://nfcore.slack.com/channels/taxprofiler
 ----------------------------------------------------------------------------------------

modules.json

@@ -2,156 +2,158 @@
     "name": "nf-core/taxprofiler",
     "homePage": "https://github.com/nf-core/taxprofiler",
     "repos": {
-        "nf-core/modules": {
+        "https://github.com/nf-core/modules.git": {
-            "git_url": "https://github.com/nf-core/modules.git",
             "modules": {
+                "nf-core": {
                     "adapterremoval": {
                         "branch": "master",
-                    "git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
-                    "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                    "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "cat/fastq": {
                         "branch": "master",
-                    "git_sha": "b034029b59b1198075da8019074bc02051a6100e"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "centrifuge/centrifuge": {
                         "branch": "master",
-                    "git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "centrifuge/kreport": {
                         "branch": "master",
-                    "git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "diamond/blastx": {
                         "branch": "master",
-                    "git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "eido/convert": {
                         "branch": "master",
-                    "git_sha": "9764eef361ded86e9242075bda64c2662421386a"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "eido/validate": {
                         "branch": "master",
-                    "git_sha": "38383cfaefc06cd35e25de99989a3e6ab9ed2980"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "fastp": {
                         "branch": "master",
-                    "git_sha": "2c70c1c1951aaf884d2e8d8d9c871db79f7b35aa"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "fastqc": {
                         "branch": "master",
-                    "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "filtlong": {
                         "branch": "master",
-                    "git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "gunzip": {
                         "branch": "master",
-                    "git_sha": "fa37e0662690c4ec4260dae282fbce08777503e6"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "kaiju/kaiju": {
                         "branch": "master",
-                    "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "kaiju/kaiju2krona": {
                         "branch": "master",
-                    "git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "kaiju/kaiju2table": {
                         "branch": "master",
-                    "git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                    "git_sha": "409a308ba46284d8ebb48c2c1befd6f6433db3f7"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "krakentools/combinekreports": {
                         "branch": "master",
-                    "git_sha": "ee0346b4d14ffdc15ce7e093ca1363cd07c9bd78"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "krakentools/kreport2krona": {
                         "branch": "master",
-                    "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
-                    "git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "krona/ktimporttext": {
                         "branch": "master",
-                    "git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "malt/run": {
                         "branch": "master",
-                    "git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "megan/rma2info": {
                         "branch": "master",
-                    "git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "metaphlan3/mergemetaphlantables": {
                         "branch": "master",
-                    "git_sha": "36bcd675ae76a379a38165898a203f4915823f4f"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "metaphlan3/metaphlan3": {
                         "branch": "master",
-                    "git_sha": "978087354eb72ac1f6e18a3f790fad9bc4d05840"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "minimap2/align": {
                         "branch": "master",
-                    "git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "minimap2/index": {
                         "branch": "master",
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "patch": "modules/nf-core/minimap2/index/minimap2-index.diff"
                     },
                     "motus/merge": {
                         "branch": "master",
-                    "git_sha": "54ff289487244bf15543ecfa62bd4df49be72b73"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "motus/profile": {
                         "branch": "master",
-                    "git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "multiqc": {
                         "branch": "master",
-                    "git_sha": "16eee433b87b303bda650131ac5a0b1ad725e166"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "porechop": {
                         "branch": "master",
-                    "git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "prinseqplusplus": {
                         "branch": "master",
-                    "git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "samtools/bam2fq": {
                         "branch": "master",
-                    "git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "samtools/view": {
                         "branch": "master",
-                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
                     "untar": {
                         "branch": "master",
-                    "git_sha": "393dbd6ddafe3f18eac02893dd4a21e4d45de679"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    }
                 }
             }
         }

modules/nf-core/cat/fastq/main.nf

@@ -1,6 +1,6 @@
 process CAT_FASTQ {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -20,9 +20,9 @@ process CAT_FASTQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
-        if (readList.size > 1) {
+        if (readList.size >= 1) {
             """
             cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
 
@@ -33,7 +33,7 @@ process CAT_FASTQ {
             """
         }
     } else {
-        if (readList.size > 2) {
+        if (readList.size >= 2) {
             def read1 = []
             def read2 = []
             readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
@@ -51,7 +51,7 @@ process CAT_FASTQ {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
         if (readList.size > 1) {
             """

modules/nf-core/centrifuge/kreport/main.nf

@@ -1,6 +1,6 @@
 process CENTRIFUGE_KREPORT {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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

@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : 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:1.13a--pyhdfd78af_1' :
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path versions

modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -58,7 +58,8 @@ versions_by_module = {}
 for process, process_versions in versions_by_process.items():
     module = process.split(":")[-1]
     try:
-        assert versions_by_module[module] == process_versions, (
+        if versions_by_module[module] != process_versions:
+            raise AssertionError(
                 "We assume that software versions are the same between all modules. "
                 "If you see this error-message it means you discovered an edge-case "
                 "and should open an issue in nf-core/tools. "

modules/nf-core/eido/convert/main.nf

@@ -1,5 +1,5 @@
 process EIDO_CONVERT {
-    tag '$samplesheet'
+    tag "$samplesheet"
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)

modules/nf-core/eido/validate/main.nf

@@ -1,5 +1,5 @@
 process EIDO_VALIDATE {
-    tag '$samplesheet'
+    tag "$samplesheet"
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)

modules/nf-core/gunzip/main.nf

@@ -1,6 +1,6 @@
 process GUNZIP {
     tag "$archive"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/kaiju/kaiju2krona/main.nf

@@ -1,6 +1,6 @@
 process KAIJU_KAIJU2KRONA {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/kaiju/kaiju2table/main.nf

@@ -1,6 +1,6 @@
 process KAIJU_KAIJU2TABLE {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/krakentools/combinekreports/main.nf

@@ -1,5 +1,5 @@
 process KRAKENTOOLS_COMBINEKREPORTS {
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/krakentools/kreport2krona/main.nf

@@ -1,6 +1,6 @@
 process KRAKENTOOLS_KREPORT2KRONA {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)

modules/nf-core/krona/ktimporttaxonomy/main.nf

@@ -1,6 +1,6 @@
 process KRONA_KTIMPORTTAXONOMY {
     tag "${meta.id}"
-    label 'process_high'
+    label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::krona=2.8" : null)

modules/nf-core/krona/ktimporttext/main.nf

@@ -1,6 +1,6 @@
 process KRONA_KTIMPORTTEXT {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/megan/rma2info/main.nf

@@ -1,6 +1,6 @@
 process MEGAN_RMA2INFO {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/minimap2/index/meta.yml

@@ -12,11 +12,21 @@ tools:
       documentation: https://github.com/lh3/minimap2#uguide
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: |
         Reference database in FASTA format.
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - mmi:
       type: file
       description: Minimap2 fasta index.

modules/nf-core/minimap2/index/minimap2-index.diff

@@ -0,0 +1,20 @@
+Changes in module 'nf-core/minimap2/index'
+--- modules/nf-core/minimap2/index/main.nf
++++ modules/nf-core/minimap2/index/main.nf
+@@ -7,11 +7,11 @@
+         'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
+ 
+     input:
+-    tuple val(meta), path(fasta)
++    path fasta
+ 
+     output:
+-    tuple val(meta), path("*.mmi"), emit: index
+-    path "versions.yml"           , emit: versions
++    path "*.mmi"        , emit: index
++    path "versions.yml" , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+
+************************************************************

modules/nf-core/motus/merge/main.nf

@@ -2,7 +2,7 @@ VERSION = '3.0.1'
 
 process MOTUS_MERGE {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/multiqc/main.nf

@@ -1,14 +1,15 @@
 process MULTIQC {
-    label 'process_medium'
+    label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : 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:1.13a--pyhdfd78af_1' :
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
+    path(extra_multiqc_config)
     path(multiqc_logo)
 
     output:
@@ -23,11 +24,13 @@ process MULTIQC {
     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 \\
-        $config \\
         $args \\
+        $config \\
+        $extra_config \\
         .
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/multiqc/meta.yml

@@ -22,6 +22,10 @@ input:
       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

modules/nf-core/samtools/view/main.nf

@@ -10,10 +10,15 @@ process SAMTOOLS_VIEW {
     input:
     tuple val(meta), path(input), path(index)
     path fasta
+    path qname
 
     output:
     tuple val(meta), path("*.bam"),  emit: bam,     optional: true
     tuple val(meta), path("*.cram"), emit: cram,    optional: true
+    tuple val(meta), path("*.sam"),  emit: sam,     optional: true
+    tuple val(meta), path("*.bai"),  emit: bai,     optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,     optional: true
+    tuple val(meta), path("*.crai"), emit: crai,    optional: true
     path  "versions.yml",            emit: versions
 
     when:
@@ -21,20 +26,23 @@ process SAMTOOLS_VIEW {
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "--reference ${fasta} -C" : ""
+    def reference = fasta ? "--reference ${fasta}" : ""
-    def file_type = input.getExtension()
+    def readnames = qname ? "--qname-file ${qname}": ""
+    def file_type = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt bam") ? "bam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    input.getExtension()
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools \\
         view \\
         --threads ${task.cpus-1} \\
         ${reference} \\
+        ${readnames} \\
         $args \\
-        $input \\
+        -o ${prefix}.${file_type} \\
-        $args2 \\
+        $input
-        > ${prefix}.${file_type}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/samtools/view/meta.yml

@@ -33,6 +33,10 @@ input:
       type: optional file
       description: Reference file the CRAM was created with
       pattern: "*.{fasta,fa}"
+  - qname:
+      type: file
+      description: Optional file with read names to output only select alignments
+      pattern: "*.{txt,list}"
 output:
   - meta:
       type: map
@@ -41,12 +45,29 @@ output:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: filtered/converted BAM/SAM file
+      description: optional filtered/converted BAM file
-      pattern: "*.{bam,sam}"
+      pattern: "*.{bam}"
   - cram:
       type: file
-      description: filtered/converted CRAM file
+      description: optional filtered/converted CRAM file
-      pattern: "*.cram"
+      pattern: "*.{cram}"
+  - sam:
+      type: file
+      description: optional filtered/converted SAM file
+      pattern: "*.{sam}"
+  # bai, csi, and crai are created with `--write-index`
+  - bai:
+      type: file
+      description: optional BAM file index
+      pattern: "*.{bai}"
+  - csi:
+      type: file
+      description: optional tabix BAM file index
+      pattern: "*.{csi}"
+  - crai:
+      type: file
+      description: optional CRAM file index
+      pattern: "*.{crai}"
   - versions:
       type: file
       description: File containing software versions
@@ -55,3 +76,4 @@ authors:
   - "@drpatelh"
   - "@joseespinosa"
   - "@FriederikeHanssen"
+  - "@priyanka-surana"

modules/nf-core/untar/main.nf

@@ -27,7 +27,7 @@ process UNTAR {
 
     ## Ensures --strip-components only applied when top level of tar contents is a directory
     ## If just files or multiple directories, place all in output
-    if [[ \$(tar -tzf ${archive} | grep "/\$" | wc -l) -eq 1 ]]; then
+    if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
         tar \\
             -C output --strip-components 1 \\
             -xzvf \\

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
@@ -159,7 +162,6 @@ try {
 }
 
 
-
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
@@ -280,6 +282,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
     version         = '1.0dev'
+    doi             = ''
 }
 
 // Load modules.config for DSL2 module specific options

nextflow_schema.json

@@ -586,12 +586,30 @@
                     "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.",

subworkflows/local/db_check.nf

@@ -3,7 +3,7 @@
 //
 
 include { DATABASE_CHECK   } from '../../modules/local/database_check'
-include { UNTAR            } from '../../modules/nf-core/modules/untar/main'
+include { UNTAR            } from '../../modules/nf-core/untar/main'
 
 workflow DB_CHECK {
     take:

subworkflows/local/input_check.nf

@@ -2,8 +2,8 @@
 // Check input samplesheet and get read channels
 //
 
-include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main'
+include { EIDO_VALIDATE } from '../../modules/nf-core/eido/validate/main'
-include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main'
+include { EIDO_CONVERT } from '../../modules/nf-core/eido/convert/main'
 
 workflow INPUT_CHECK {
     take:

subworkflows/local/longread_hostremoval.nf

@@ -2,10 +2,10 @@
 // Remove host reads via alignment and export off-target reads
 //
 
-include { MINIMAP2_INDEX             } from '../../modules/nf-core/modules/minimap2/index/main'
+include { MINIMAP2_INDEX             } from '../../modules/nf-core/minimap2/index/main'
-include { MINIMAP2_ALIGN             } from '../../modules/nf-core/modules/minimap2/align/main'
+include { MINIMAP2_ALIGN             } from '../../modules/nf-core/minimap2/align/main'
-include { SAMTOOLS_VIEW              } from '../../modules/nf-core/modules/samtools/view/main'
+include { SAMTOOLS_VIEW              } from '../../modules/nf-core/samtools/view/main'
-include { SAMTOOLS_BAM2FQ            } from '../../modules/nf-core/modules/samtools/bam2fq/main'
+include { SAMTOOLS_BAM2FQ            } from '../../modules/nf-core/samtools/bam2fq/main'
 
 workflow LONGREAD_HOSTREMOVAL {
     take:
@@ -33,7 +33,7 @@ workflow LONGREAD_HOSTREMOVAL {
         }
 
 
-    SAMTOOLS_VIEW ( ch_minimap2_mapped , [] )
+    SAMTOOLS_VIEW ( ch_minimap2_mapped , [], [] )
     ch_versions      = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
 
     SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )

subworkflows/local/longread_preprocessing.nf

@@ -2,9 +2,9 @@
 // Process long raw reads with porechop
 //
 
-include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
+include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
-include { PORECHOP                   } from '../../modules/nf-core/modules/porechop/main'
+include { PORECHOP                   } from '../../modules/nf-core/porechop/main'
-include { FILTLONG                   } from '../../modules/nf-core/modules/filtlong/main'
+include { FILTLONG                   } from '../../modules/nf-core/filtlong/main'
 
 workflow LONGREAD_PREPROCESSING {
     take:

subworkflows/local/profiling.nf

@@ -2,15 +2,15 @@
 // Run profiling
 //
 
-include { MALT_RUN                              } from '../../modules/nf-core/modules/malt/run/main'
+include { MALT_RUN                              } from '../../modules/nf-core/malt/run/main'
-include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV  } from '../../modules/nf-core/modules/megan/rma2info/main'
+include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV  } from '../../modules/nf-core/megan/rma2info/main'
-include { KRAKEN2_KRAKEN2                       } from '../../modules/nf-core/modules/kraken2/kraken2/main'
+include { KRAKEN2_KRAKEN2                       } from '../../modules/nf-core/kraken2/kraken2/main'
-include { CENTRIFUGE_CENTRIFUGE                 } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
+include { CENTRIFUGE_CENTRIFUGE                 } from '../../modules/nf-core/centrifuge/centrifuge/main'
-include { CENTRIFUGE_KREPORT                    } from '../../modules/nf-core/modules/centrifuge/kreport/main'
+include { CENTRIFUGE_KREPORT                    } from '../../modules/nf-core/centrifuge/kreport/main'
-include { METAPHLAN3_METAPHLAN3                 } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main'
+include { METAPHLAN3_METAPHLAN3                 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
-include { KAIJU_KAIJU                           } from '../../modules/nf-core/modules/kaiju/kaiju/main'
+include { KAIJU_KAIJU                           } from '../../modules/nf-core/kaiju/kaiju/main'
-include { DIAMOND_BLASTX                        } from '../../modules/nf-core/modules/diamond/blastx/main'
+include { DIAMOND_BLASTX                        } from '../../modules/nf-core/diamond/blastx/main'
-include { MOTUS_PROFILE                         } from '../../modules/nf-core/modules/motus/profile/main'
+include { MOTUS_PROFILE                         } from '../../modules/nf-core/motus/profile/main'
 
 workflow PROFILING {
     take:

subworkflows/local/shortread_adapterremoval.nf

@@ -2,9 +2,9 @@
 // Process short raw reads with AdapterRemoval
 //
 
-include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE       } from '../../modules/nf-core/modules/adapterremoval/main'
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE       } from '../../modules/nf-core/adapterremoval/main'
-include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED       } from '../../modules/nf-core/modules/adapterremoval/main'
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED       } from '../../modules/nf-core/adapterremoval/main'
-include { CAT_FASTQ                                     } from '../../modules/nf-core/modules/cat/fastq/main'
+include { CAT_FASTQ                                     } from '../../modules/nf-core/cat/fastq/main'
 
 workflow SHORTREAD_ADAPTERREMOVAL {
 

subworkflows/local/shortread_complexityfiltering.nf

@@ -2,8 +2,8 @@
 // Check input samplesheet and get read channels
 //
 
-include { BBMAP_BBDUK     } from '../../modules/nf-core/modules/bbmap/bbduk/main'
+include { BBMAP_BBDUK     } from '../../modules/nf-core/bbmap/bbduk/main'
-include { PRINSEQPLUSPLUS } from '../../modules/nf-core/modules/prinseqplusplus/main'
+include { PRINSEQPLUSPLUS } from '../../modules/nf-core/prinseqplusplus/main'
 
 workflow SHORTREAD_COMPLEXITYFILTERING {
     take:

subworkflows/local/shortread_fastp.nf

@@ -2,8 +2,8 @@
 // Process short raw reads with FastP
 //
 
-include { FASTP as FASTP_SINGLE       } from '../../modules/nf-core/modules/fastp/main'
+include { FASTP as FASTP_SINGLE       } from '../../modules/nf-core/fastp/main'
-include { FASTP as FASTP_PAIRED       } from '../../modules/nf-core/modules/fastp/main'
+include { FASTP as FASTP_PAIRED       } from '../../modules/nf-core/fastp/main'
 
 workflow SHORTREAD_FASTP {
     take:

subworkflows/local/shortread_hostremoval.nf

@@ -2,8 +2,8 @@
 // Remove host reads via alignment and export off-target reads
 //
 
-include { BOWTIE2_BUILD             } from '../../modules/nf-core/modules/bowtie2/build/main'
+include { BOWTIE2_BUILD             } from '../../modules/nf-core/bowtie2/build/main'
-include { BOWTIE2_ALIGN             } from '../../modules/nf-core/modules/bowtie2/align/main'
+include { BOWTIE2_ALIGN             } from '../../modules/nf-core/bowtie2/align/main'
 
 workflow SHORTREAD_HOSTREMOVAL {
     take: