From bfb1d70cf4121449595ec39ea961abce9032be01 Mon Sep 17 00:00:00 2001
From: nickhsmith <smithnickh@gmail.com>
Date: Wed, 17 Nov 2021 16:07:06 +0100
Subject: [PATCH 1/2] Update nextflow_schema.json

---
 nextflow_schema.json | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 673a7494b4..108ea4555e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -11,20 +11,9 @@
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
             "required": [
-                "input",
                 "step"
             ],
             "properties": {
-                "input": {
-                    "type": "string",
-                    "format": "file-path",
-                    "mimetype": "text/csv",
-                    "pattern": "\\.csv$",
-                    "schema": "assets/schema_input.json",
-                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
-                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).",
-                    "fa_icon": "fas fa-file-csv"
-                },
                 "step": {
                     "type": "string",
                     "default": "mapping",
@@ -40,6 +29,16 @@
                         "controlfreec"
                     ]
                 },
+                "input": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/csv",
+                    "pattern": "\\.csv$",
+                    "schema": "assets/schema_input.json",
+                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).",
+                    "fa_icon": "fas fa-file-csv"
+                },
                 "outdir": {
                     "type": "string",
                     "description": "Path to the output directory where the results will be saved.",
@@ -796,4 +795,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
\ No newline at end of file
+}

From 7898b0f57d98cde561f66ae025df8c01f5568082 Mon Sep 17 00:00:00 2001
From: nickhsmith <smithnickh@gmail.com>
Date: Wed, 17 Nov 2021 16:12:14 +0100
Subject: [PATCH 2/2] Update WorkflowMain.groovy

remove requirement for input.csv
---
 lib/WorkflowMain.groovy | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 1875428ed1..2831a2db00 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -71,12 +71,6 @@ class WorkflowMain {
 
         // Check the hostnames against configured profiles
         NfcoreTemplate.hostName(workflow, params, log)
-
-        // Check input has been provided
-        if (!params.input) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
-            System.exit(1)
-        }
     }
 
     //