updating config

number-25 · number-25 · commit 2b88ddb6c226 · 2025-12-16T08:07:48.000+10:00
diff --git a/conf/test.config b/conf/test.config
@@ -82,7 +82,7 @@ params {
     sqanti_qc_intron_junctions      = true
     sqanti_qc_intron_path           = null
     extra_sqanti_qc_options         = null
-    help                            = true
+    help                            = false
 }
 
 validation {
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -81,7 +81,7 @@ params {
     sqanti_qc_intron_junctions      = false
     sqanti_qc_intron_path           = null
     extra_sqanti_qc_options         = null
-    help                            = true
+    help                            = false
 }
 
 validation {
diff --git a/conf/test_gzipped.config b/conf/test_gzipped.config
@@ -82,7 +82,7 @@ params {
     sqanti_qc_intron_junctions      = true
     sqanti_qc_intron_path           = null
     extra_sqanti_qc_options         = null
-    help                            = true
+    help                            = false
 }
 
 validation {
diff --git a/main.nf b/main.nf
@@ -30,15 +30,15 @@ workflow{
    // validateParameters()
     log.info paramsSummaryLog(workflow)
 
-/*    if (params.help) {
+    if (params.help) {
         log.info paramsHelp(
             beforeText: "Welcome to LongTranscriptomics, I see you are seeking help.",
             afterText: "Farewell, hopefully this was helpful.",
             command: "nextflow run . -profile <profile> --outdir <outdir>",
         )
         exit 0
     }
-*/
+
 
     DIRECTRNA ()
 }
diff --git a/nextflow.config b/nextflow.config
@@ -124,7 +124,7 @@ params {
     plaintext_email                 = false
     monochrome_logs                 = false
     hook_url                        = null
-    help                            = true
+    help                            = false
     version                         = false
     //pipelines_testdata_base_path  = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -72,6 +72,13 @@
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
+                "help": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Show the help message for the pipeline.",
+                    "fa_icon": "fas fa-question-circle",
+                    "help_text": "Welcome to LongTranscriptomics, I see you are seeking help, these are  a list of basic parameters."
+                },
                 "sequencing_type": {
                     "type": "string",
                     "default": "ont-drna",
diff --git a/null/pipeline_info/execution_trace_2025-12-10_16-48-28.txt b/null/pipeline_info/execution_trace_2025-12-10_16-48-28.txt
@@ -0,0 +1 @@
+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
diff --git a/null/pipeline_info/execution_trace_2025-12-10_16-48-54.txt b/null/pipeline_info/execution_trace_2025-12-10_16-48-54.txt
@@ -0,0 +1 @@
+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
diff --git a/null/pipeline_info/execution_trace_2025-12-10_17-02-22.txt b/null/pipeline_info/execution_trace_2025-12-10_17-02-22.txt
@@ -0,0 +1 @@
+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar

Original file line number	Diff line number	Diff line change
`@@ -82,7 +82,7 @@ params {`
`82`	`82`	`sqanti_qc_intron_junctions = true`
`83`	`83`	`sqanti_qc_intron_path = null`
`84`	`84`	`extra_sqanti_qc_options = null`
`85`		`- help = true`
	`85`	`+ help = false`
`86`	`86`	`}`
`87`	`87`
`88`	`88`	`validation {`
Original file line number	Diff line number	Diff line change
`@@ -81,7 +81,7 @@ params {`
`81`	`81`	`sqanti_qc_intron_junctions = false`
`82`	`82`	`sqanti_qc_intron_path = null`
`83`	`83`	`extra_sqanti_qc_options = null`
`84`		`- help = true`
	`84`	`+ help = false`
`85`	`85`	`}`
`86`	`86`
`87`	`87`	`validation {`
Original file line number	Diff line number	Diff line change
`@@ -30,15 +30,15 @@ workflow{`
`30`	`30`	`// validateParameters()`
`31`	`31`	`log.info paramsSummaryLog(workflow)`
`32`	`32`
`33`		`-/* if (params.help) {`
	`33`	`+ if (params.help) {`
`34`	`34`	`log.info paramsHelp(`
`35`	`35`	`beforeText: "Welcome to LongTranscriptomics, I see you are seeking help.",`
`36`	`36`	`afterText: "Farewell, hopefully this was helpful.",`
`37`	`37`	`command: "nextflow run . -profile <profile> --outdir <outdir>",`
`38`	`38`	`)`
`39`	`39`	`exit 0`
`40`	`40`	`}`
`41`		`-*/`
	`41`	`+`
`42`	`42`
`43`	`43`	`DIRECTRNA ()`
`44`	`44`	`}`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar`