Added nextflow command line

aolveraNIH · aolveraNIH · commit 0b09e9f10991 · 2025-04-17T13:12:00.000-05:00
diff --git a/GoogleCloud/Submodule_02_basic_assembly.ipynb b/GoogleCloud/Submodule_02_basic_assembly.ipynb
@@ -180,8 +180,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!NXF_VER=22.10.1 ./nextflow run ./TransPi/TransPi.nf \\\n",
-    "-profile docker --k 17,25,43 --maxReadLen 50 --all "
+    "!nextflow run main.nf --input test_samplesheet.csv -profile test,docker -c conf/test_params.config --run_mode full "
    ]
   },
   {
@@ -345,7 +344,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }
diff --git a/GoogleCloud/Submodule_04_google_batch_assembly.ipynb b/GoogleCloud/Submodule_04_google_batch_assembly.ipynb
@@ -416,8 +416,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!NXF_VER=22.10.1 ./nextflow run ./TransPi/TransPi.nf \\\n",
-    "-profile gcb --k 17,25,43 --maxReadLen 50 --all -resume"
+    "!nextflow run main.nf --input test_samplesheet.csv -profile test,docker,gbatch -c conf/test_params.config --run_mode full "
    ]
   },
   {

Original file line number	Diff line number	Diff line change
`@@ -180,8 +180,7 @@`
`180`	`180`	`"metadata": {},`
`181`	`181`	`"outputs": [],`
`182`	`182`	`"source": [`
`183`		`- "!NXF_VER=22.10.1 ./nextflow run ./TransPi/TransPi.nf \\\n",`
`184`		`- "-profile docker --k 17,25,43 --maxReadLen 50 --all "`
	`183`	`+ "!nextflow run main.nf --input test_samplesheet.csv -profile test,docker -c conf/test_params.config --run_mode full "`
`185`	`184`	`]`
`186`	`185`	`},`
`187`	`186`	`{`
`@@ -345,7 +344,11 @@`
`345`	`344`	`]`
`346`	`345`	`}`
`347`	`346`	`],`
`348`		`- "metadata": {},`
	`347`	`+ "metadata": {`
	`348`	`+ "language_info": {`
	`349`	`+ "name": "python"`
	`350`	`+ }`
	`351`	`+ },`
`349`	`352`	`"nbformat": 4,`
`350`	`353`	`"nbformat_minor": 5`
`351`	`354`	`}`
Original file line number	Diff line number	Diff line change
`@@ -416,8 +416,7 @@`
`416`	`416`	`"metadata": {},`
`417`	`417`	`"outputs": [],`
`418`	`418`	`"source": [`
`419`		`- "!NXF_VER=22.10.1 ./nextflow run ./TransPi/TransPi.nf \\\n",`
`420`		`- "-profile gcb --k 17,25,43 --maxReadLen 50 --all -resume"`
	`419`	`+ "!nextflow run main.nf --input test_samplesheet.csv -profile test,docker,gbatch -c conf/test_params.config --run_mode full "`
`421`	`420`	`]`
`422`	`421`	`},`
`423`	`422`	`{`