Bump modules (#161)

* bump modules

* update subwf, include nf-teams

* fix errors

Author: matthdsm

assets/adaptivecard.json

@@ -62,7 +62,6 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         PREPROCESSING.out.multiqc_report,
     )
 

assets/slackreport.json

@@ -103,7 +103,7 @@
                     },
                     "samtools/coverage": {
                         "branch": "master",
-                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
+                        "git_sha": "440edf75d8782913115a7b72a88392a227f72cc1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
                     },
@@ -170,7 +170,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "65f5e638d901a51534c68fd5c1c19e8112fb4df1",
+                        "git_sha": "f0b535b3ae20080f8db03dd5388876ad1ec29d70",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

main.nf

@@ -269,13 +269,23 @@ manifest {
 // Nextflow plugins
 plugins {
     id 'nf-schema@2.6.1'
+    id 'nf-teams@0.1.0'
 }
 
 validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs      = params.monochrome_logs
 }
 
+// TODO remove this once minimal nf-version is 26.0X with strict syntax.
+teams {
+    enabled            = true
+    webHook {
+        url = params.hook_url ? params.hook_url : System.getenv('TEAMS_WEBHOOK_URL')
+    }
+    onComplete.enabled = true
+}
+
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 

modules.json

@@ -14,7 +14,6 @@ include { samplesheetToList       } from 'plugin/nf-schema'
 include { paramsHelp              } from 'plugin/nf-schema'
 include { completionEmail         } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary       } from '../../nf-core/utils_nfcore_pipeline'
-include { imNotification          } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE   } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
 
@@ -99,7 +98,6 @@ workflow PIPELINE_COMPLETION {
     plaintext_email // boolean: Send plain-text email instead of HTML
     outdir //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url //  string: hook URL for notifications
     multiqc_report //  string: Path to MultiQC report
 
     main:
@@ -123,9 +121,6 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
     }
 
     workflow.onError {