add shebang to all main Nextflow script

maxulysse · maxulysse · commit bc8829a90421 · 2024-10-03T19:07:35.000+02:00
Signed-off-by: maxulysse &lt;max.u.garcia@gmail.com&gt;
diff --git a/hands-on/final_main.nf b/hands-on/final_main.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Define the default parameters
  */
diff --git a/hello-nextflow/hello-gatk.nf b/hello-nextflow/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/hello-modules.nf b/hello-nextflow/hello-modules.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/hello-nf-test.nf b/hello-nextflow/hello-nf-test.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 // Include modules
 include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf'
 include { GATK_HAPLOTYPECALLER } from './modules/local/gatk/haplotypecaller/main.nf'
diff --git a/hello-nextflow/hello-world.nf b/hello-nextflow/hello-world.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 process sayHello {
 
     output: 
diff --git a/hello-nextflow/scripts/hello-gatk-1.nf b/hello-nextflow/scripts/hello-gatk-1.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-gatk-2.nf b/hello-nextflow/scripts/hello-gatk-2.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-gatk-3.nf b/hello-nextflow/scripts/hello-gatk-3.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-gatk-4.nf b/hello-nextflow/scripts/hello-gatk-4.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-gatk-5.nf b/hello-nextflow/scripts/hello-gatk-5.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-gatk-6.nf b/hello-nextflow/scripts/hello-gatk-6.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-modules-1.nf b/hello-nextflow/scripts/hello-modules-1.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Generate BAM index file
  */
diff --git a/hello-nextflow/scripts/hello-modules-2.nf b/hello-nextflow/scripts/hello-modules-2.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Call variants with GATK HapolotypeCaller in GVCF mode
  */
diff --git a/hello-nextflow/scripts/hello-modules-3.nf b/hello-nextflow/scripts/hello-modules-3.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 // Include modules
 include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf'
 include { GATK_HAPLOTYPECALLER } from './modules/local/gatk/haplotypecaller/main.nf'
diff --git a/hello-nextflow/scripts/hello-world-1.nf b/hello-nextflow/scripts/hello-world-1.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 process sayHello {
 
     output: 
diff --git a/hello-nextflow/scripts/hello-world-2.nf b/hello-nextflow/scripts/hello-world-2.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Use echo to print 'Hello World!' to standard out
  */
diff --git a/hello-nextflow/scripts/hello-world-3.nf b/hello-nextflow/scripts/hello-world-3.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Use echo to print 'Hello World!' to standard out
  */
diff --git a/hello-nextflow/scripts/hello-world-4.nf b/hello-nextflow/scripts/hello-world-4.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Use echo to print 'Hello World!' to standard out
  */
diff --git a/hello-nextflow/scripts/hello-world-5.nf b/hello-nextflow/scripts/hello-world-5.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Use echo to print 'Hello World!' to standard out
  */
diff --git a/hello-nextflow/scripts/hello-world-6.nf b/hello-nextflow/scripts/hello-world-6.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-world-7.nf b/hello-nextflow/scripts/hello-world-7.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-world-8.nf b/hello-nextflow/scripts/hello-world-8.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/hello-nextflow/scripts/hello-world-9.nf b/hello-nextflow/scripts/hello-world-9.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/nf-training-advanced/groovy/main.nf b/nf-training-advanced/groovy/main.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 include { FASTP } from './modules/local/fastp/main.nf'
 
 workflow {
diff --git a/nf-training-advanced/metadata/main.nf b/nf-training-advanced/metadata/main.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 workflow {
     Channel.fromFilePairs("data/reads/*/*_R{1,2}.fastq.gz")
     | view
diff --git a/nf-training-advanced/operators/main.nf b/nf-training-advanced/operators/main.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 workflow {
     Channel.of( 1, 2, 3, 4, 5 )
     | map { it * it }
diff --git a/nf-training-advanced/structure/main.nf b/nf-training-advanced/structure/main.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 workflow {
     names = Channel.of("Argente", "Absolon", "Chowne")
 }
diff --git a/nf-training/script1.nf b/nf-training/script1.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 params.reads = "$projectDir/data/ggal/gut_{1,2}.fq"
 params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
 params.multiqc = "$projectDir/multiqc"
diff --git a/nf-training/script2.nf b/nf-training/script2.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * pipeline input parameters
  */
diff --git a/nf-training/script3.nf b/nf-training/script3.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * pipeline input parameters
  */
diff --git a/nf-training/script4.nf b/nf-training/script4.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * pipeline input parameters
  */
diff --git a/nf-training/script5.nf b/nf-training/script5.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * pipeline input parameters
  */
diff --git a/nf-training/script6.nf b/nf-training/script6.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * pipeline input parameters
  */
diff --git a/nf-training/script7.nf b/nf-training/script7.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * pipeline input parameters
  */
diff --git a/nf-training/snippet.nf b/nf-training/snippet.nf
@@ -1,2 +1,4 @@
+#!/usr/bin/env nextflow
+
 ch = Channel.of("1","2","3")
 ch.view() 
diff --git a/troubleshoot/exercise1/hello-gatk.nf b/troubleshoot/exercise1/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/troubleshoot/exercise2/hello-gatk.nf b/troubleshoot/exercise2/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/troubleshoot/exercise3/hello-gatk.nf b/troubleshoot/exercise3/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/troubleshoot/exercise4/hello-gatk.nf b/troubleshoot/exercise4/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/troubleshoot/exercise5/hello-gatk.nf b/troubleshoot/exercise5/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/troubleshoot/exercise6/hello-gatk.nf b/troubleshoot/exercise6/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */
diff --git a/troubleshoot/hello-gatk.nf b/troubleshoot/hello-gatk.nf
@@ -1,3 +1,5 @@
+#!/usr/bin/env nextflow
+
 /*
  * Pipeline parameters
  */

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+#!/usr/bin/env nextflow`
	`2`	`+`
`1`	`3`	`/*`
`2`	`4`	`* Define the default parameters`
`3`	`5`	`*/`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+#!/usr/bin/env nextflow`
	`2`	`+`
`1`	`3`	`// Include modules`
`2`	`4`	`include { SAMTOOLS_INDEX } from './modules/local/samtools/index/main.nf'`
`3`	`5`	`include { GATK_HAPLOTYPECALLER } from './modules/local/gatk/haplotypecaller/main.nf'`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+#!/usr/bin/env nextflow`
	`2`	`+`
`1`	`3`	`process sayHello {`
`2`	`4`
`3`	`5`	`output:`