Merge branch 'main' of https://github.com/aineniamh/piranha into main

polio-nanopore · Oct 24, 2023 · 2a973be · 2a973be
2 parents e5b6280 + 71a76c8
commit 2a973be
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Showing 4 changed files with 79 additions and 17 deletions.
diff --git a/main.nf b/main.nf
@@ -9,11 +9,16 @@ process run_piranha {
         path run_dir
 
     output:
-        path "piranha_output"
+        path "piranha_report.html"
+        path "barcode_reports"
+        path "detailed_run_report.csv"
+        path "published_data"
 
     script:
     """
     piranha -b ${barcodes_csv} -i ${run_dir} -o piranha_output --tempdir piranha_tmp -t ${task.cpus}
+    mv piranha_output/* .
+    mv report.html piranha_report.html
     """
 
 }
@@ -23,4 +28,4 @@ workflow {
     run_dir = Channel.of(file("${params.run_dir}", type: "dir", checkIfExists:true))
 
     run_piranha(barcodes_csv, run_dir)
-}
+}
diff --git a/nextflow.config b/nextflow.config
@@ -49,7 +49,7 @@ manifest {
     description     = 'Polio investigation resource automating nanopore haplotype analysis.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.1'
+    version         = '1.1'
 }
 
 
@@ -73,9 +73,6 @@ profiles {
     standard {
         docker {
             enabled = true
-            // this ensures container is run as host user and group, but
-            //    also adds host user to the within-container group
-            runOptions = "--user \$(id -u):\$(id -g) --group-add 100 --env XDG_CACHE_HOME=\$NXF_TASK_WORKDIR/.cache"
         }
     }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -4,6 +4,7 @@
   "title": "polio-nanopore/piranha",
   "description": "Polio investigation resource automating nanopore haplotype analysis.",
   "url": "https://github.com/polio-nanopore/piranha",
+  "demo_url": "https://raw.githubusercontent.com/polio-nanopore/piranha/main/piranha/test/pak_run",
   "type": "object",
   "definitions": {
     "input_options": {
@@ -15,35 +16,89 @@
         "barcodes_csv": {
           "type": "string",
           "format": "path",
-          "title": "BARCODES_CSV",
+          "title": "Barcodes",
           "description": "A CSV file with barcode and sample columns.",
           "help_text": ".",
-          "demo_data": "piranha/test/pak_run/barcodes01.csv"
+          "demo_data": "barcodes01.csv"
         },
         "run_dir": {
           "type": "string",
           "format": "path",
-          "title": "RUN_DIR",
+          "title": "Run directory",
           "description": "A directory containing a directory of fastq for a each barcode in a run.",
           "help_text": "A directory containing subdirectories of fastq files as created by MinKNOW.",
-          "demo_data": "piranha/test/pak_run/demultiplexed"
+          "demo_data": "demultiplexed"
         }
       },
-      "oneOf": [
+      "allOf": [
         {
           "required": [
-            "run_dir",
-            "barcodes_csv"
+            "barcodes_csv",
+            "run_dir"
           ]
         }
       ]
     },
-    "allOf": [
-      {
-        "$ref": "#/definitions/input_options"
+    "output_options": {
+      "title": "Output Options",
+      "type": "object",
+      "description": "Parameters for saving and naming workflow outputs.",
+      "default": "",
+      "properties": {
+        "out_dir": {
+          "type": "string",
+          "format": "directory-path",
+          "default": "output",
+          "title": "Output folder name",
+          "description": "Directory for output of all user-facing files."
+        }
+      }
+    },
+    "advanced_options": {
+      "title": "Advanced Options",
+      "type": "object",
+      "description": "Advanced options for configuring processes inside the workflow.",
+      "default": "",
+      "properties": {
       }
-    ]
+    },
+    "miscellaneous_options": {
+      "title": "Miscellaneous Options",
+      "type": "object",
+      "fa_icon": "fas fa-file-import",
+      "description": "Everything else.",
+      "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+      "properties": {
+        "help": {
+          "type": "boolean",
+          "title": "Display help text",
+          "fa_icon": "fas fa-question-circle",
+          "hidden": true
+        },
+        "version": {
+          "type": "boolean",
+          "title": "Display version",
+          "description": "Display version and exit.",
+          "fa_icon": "fas fa-question-circle",
+          "hidden": true
+        }
+      }
+    }
   },
+  "allOf": [
+    {
+      "$ref": "#/definitions/input_options"
+    },
+    {
+      "$ref": "#/definitions/output_options"
+    },
+    {
+      "$ref": "#/definitions/advanced_options"
+    },
+    {
+      "$ref": "#/definitions/miscellaneous_options"
+    }
+  ],
   "properties": {
     "aws_image_prefix": {
       "type": "string",

diff --git a/piranha/test/nextflow.config b/piranha/test/nextflow.config
@@ -0,0 +1,5 @@
+params {
+    barcodes_csv = "pak_run/barcodes01.csv"
+    run_dir = "pak_run/demultiplexed"
+    out_dir = "output"
+}