Produce a markdown document bundle to facilitate downstream analysis

nf-core · Oct 12, 2023 · f3fe4df · f3fe4df
1 parent c9d5328
commit f3fe4df
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Showing 5 changed files with 76 additions and 7 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -399,6 +399,14 @@ process {
         ]
     }
 
+    withName: MAKE_REPORT_BUNDLE {
+        publishDir = [
+            path: { "${params.outdir}/report" },
+            mode: params.publish_dir_mode,
+            pattern: '*.zip'
+        ]
+    }
+
     withName: CUSTOM_MATRIXFILTER {
         publishDir = [
             enabled: false

diff --git a/modules.json b/modules.json
@@ -67,7 +67,7 @@
                     },
                     "rmarkdownnotebook": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "4e640839b1076da7c2a2a4a8f160815e00eedfba",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/app": {
@@ -94,6 +94,11 @@
                         "branch": "master",
                         "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
                         "installed_by": ["modules"]
+                    },
+                    "zip": {
+                        "branch": "master",
+                        "git_sha": "363ab4f7ed481242f5b1d73f81ffe76cea33fdaf",
+                        "installed_by": ["modules"]
                     }
                 }
             },

diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf
diff --git a/tower.yml b/tower.yml
@@ -1,6 +1,8 @@
 reports:
   "**/report/*.html":
     display: "Final differential abundance report"
+ "**/report/*.zip":
+    display: "Report bundle (markdown + input files)"
   pipeline_info/**:
     display: "Pipeline run info"
   "**/plots/exploratory/**/html/*.html":

diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
@@ -127,6 +127,7 @@ include { AFFY_JUSTRMA as AFFY_JUSTRMA_RAW                  } from '../modules/n
 include { AFFY_JUSTRMA as AFFY_JUSTRMA_NORM                 } from '../modules/nf-core/affy/justrma/main'
 include { PROTEUS_READPROTEINGROUPS as PROTEUS              } from '../modules/nf-core/proteus/readproteingroups/main'
 include { GEOQUERY_GETGEO                                   } from '../modules/nf-core/geoquery/getgeo/main'
+include { ZIP as MAKE_REPORT_BUNDLE                         } from '../modules/nf-core/zip/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -584,6 +585,15 @@ workflow DIFFERENTIALABUNDANCE {
         ch_report_input_files
     )
 
+    // Make a report bundle comprising the markdown document and all necessary
+    // input files
+
+    MAKE_REPORT_BUNDLE(
+        RMARKDOWNNOTEBOOK.out.parameterised_notebook
+            .combine(ch_report_input_files)
+            .map{[it[0], it[1..-1]]}
+    )
+
 }
 
 /*