Updated nextflow command to run with files in denovotranscript folder

aolveraNIH · aolveraNIH · commit 0181be9d72a6 · 2025-05-06T10:07:33.000-06:00
diff --git a/GoogleCloud/Submodule_3_basic_assembly.ipynb b/GoogleCloud/Submodule_3_basic_assembly.ipynb
@@ -67,7 +67,8 @@
    "id": "7be8ab78",
    "metadata": {},
    "source": [
-    "## Learning Objectives"
+    "## Learning Objectives\n",
+    "\n"
    ]
   },
   {
@@ -196,7 +197,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! nextflow run main.nf --input test_samplesheet.csv -profile gbatch --run_mode full"
+    "! nextflow run ../denovotranscript/main.nf --input ../denovotranscript/test_samplesheet_gcp.csv -profile gbatch --run_mode full"
    ]
   },
   {

Original file line number	Diff line number	Diff line change
`@@ -67,7 +67,8 @@`
`67`	`67`	`"id": "7be8ab78",`
`68`	`68`	`"metadata": {},`
`69`	`69`	`"source": [`
`70`		`- "## Learning Objectives"`
	`70`	`+ "## Learning Objectives\n",`
	`71`	`+ "\n"`
`71`	`72`	`]`
`72`	`73`	`},`
`73`	`74`	`{`
`@@ -196,7 +197,7 @@`
`196`	`197`	`"metadata": {},`
`197`	`198`	`"outputs": [],`
`198`	`199`	`"source": [`
`199`		`- "! nextflow run main.nf --input test_samplesheet.csv -profile gbatch --run_mode full"`
	`200`	`+ "! nextflow run ../denovotranscript/main.nf --input ../denovotranscript/test_samplesheet_gcp.csv -profile gbatch --run_mode full"`
`200`	`201`	`]`
`201`	`202`	`},`
`202`	`203`	`{`