Integrate multiqcsav to pipeline

main.nf

@@ -57,6 +57,7 @@ workflow NFCORE_DEMULTIPLEX {
     fastq_idx                   = DEMULTIPLEX.out.fastq_idx
     undetermined                = DEMULTIPLEX.out.undetermined
     undetermined_idx            = DEMULTIPLEX.out.undetermined_idx
+    multiqcsav_report           = DEMULTIPLEX.out.multiqcsav_report
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -120,6 +121,7 @@ workflow {
     fastq_idx                 = NFCORE_DEMULTIPLEX.out.fastq_idx
     undetermined              = NFCORE_DEMULTIPLEX.out.undetermined
     undetermined_idx          = NFCORE_DEMULTIPLEX.out.undetermined_idx
+    multiqcsav_report         = NFCORE_DEMULTIPLEX.out.multiqcsav_report
 
 }
 
@@ -176,7 +178,6 @@ output {
         path { "multiqc/" }
     }
 
-
     checkqc_reports {
         path { meta, _report ->
             def lane_dir = meta.lane ? "${meta.id}/L00${meta.lane}" : "${meta.id}"
@@ -237,6 +238,10 @@ output {
             }
         }
     }
+
+    multiqcsav_report {
+        path { "multiqcsav/" }
+    }
 }
 
 /*

modules.json

@@ -12,12 +12,12 @@
                     },
                     "bcl2fastq": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "5409e115dc29a5336152edcdd2fb65b2e8230380",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "bclconvert": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "e4a7e011bee58ded839f4da6bf9bb3fbfbebdebd",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "cellranger/mkfastq": {
@@ -70,6 +70,11 @@
                         "git_sha": "80cba9452fb1e9bb79884976fa1ca0e671949aa2",
                         "installed_by": ["modules"]
                     },
+                    "multiqcsav": {
+                        "branch": "master",
+                        "git_sha": "cb9f4bec379866ca560f7f79d9a9a06bea8c9b51",
+                        "installed_by": ["bcl_demultiplex"]
+                    },
                     "samshee": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
@@ -96,9 +101,8 @@
                 "nf-core": {
                     "bcl_demultiplex": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
-                        "installed_by": ["subworkflows"],
-                        "patch": "subworkflows/nf-core/bcl_demultiplex/bcl_demultiplex.diff"
+                        "git_sha": "f3086dae4abcf5aa695f65e352b9293b76b693ee",
+                        "installed_by": ["subworkflows"]
                     },
                     "fastq_contam_seqtk_kraken": {
                         "branch": "master",