diff --git a/docs/hello_nextflow/02_hello_world.md b/docs/hello_nextflow/02_hello_world.md
index 4441aa141f..f6f8842f80 100644
--- a/docs/hello_nextflow/02_hello_world.md
+++ b/docs/hello_nextflow/02_hello_world.md
@@ -78,6 +78,7 @@ process sayHello {
     output:
         stdout
 
+    script:
     """
     echo 'Hello World!'
     """
@@ -112,6 +113,7 @@ process sayHello {
     output:
         stdout
 
+    script:
     """
     echo 'Hello World!'
     """
@@ -749,6 +751,7 @@ process convertToUpper {
     output:
         path "UPPER-${input_file}"
 
+    script:
     """
     cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
     """
@@ -945,6 +948,7 @@ process sayHello {
     output:
         path "output.txt"
 
+    script:
     """
     echo '$greeting' > "output.txt"
     """
@@ -964,6 +968,7 @@ process sayHello {
     output:
         path "${greeting}-output.txt"
 
+    script:
     """
     echo '$greeting' > '$greeting-output.txt'
     """
diff --git a/docs/hello_nextflow/04_hello_genomics.md b/docs/hello_nextflow/04_hello_genomics.md
index 59be62228e..64252116ad 100644
--- a/docs/hello_nextflow/04_hello_genomics.md
+++ b/docs/hello_nextflow/04_hello_genomics.md
@@ -189,6 +189,7 @@ process SAMTOOLS_INDEX {
     output:
         path "${input_bam}.bai"
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -312,6 +313,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.vcf"     , emit: vcf
         path "${input_bam}.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/docs/hello_nextflow/05_hello_operators.md b/docs/hello_nextflow/05_hello_operators.md
index 4e1d889ed7..185b465f60 100644
--- a/docs/hello_nextflow/05_hello_operators.md
+++ b/docs/hello_nextflow/05_hello_operators.md
@@ -422,6 +422,7 @@ process GATK_GENOMICSDB {
     output:
         path "${cohort_name}_gdb"
 
+    script:
     """
     gatk GenomicsDBImport \
         -V ${all_gvcfs} \
diff --git a/docs/hello_nextflow/07_hello_modules.md b/docs/hello_nextflow/07_hello_modules.md
index 3fb91b6076..91726fc94d 100644
--- a/docs/hello_nextflow/07_hello_modules.md
+++ b/docs/hello_nextflow/07_hello_modules.md
@@ -175,6 +175,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -295,6 +296,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/containers/solutions/hello-containers-3.nf b/hello-nextflow/containers/solutions/hello-containers-3.nf
index 4335547474..cdefb478d9 100644
--- a/hello-nextflow/containers/solutions/hello-containers-3.nf
+++ b/hello-nextflow/containers/solutions/hello-containers-3.nf
@@ -43,6 +43,7 @@ process cowSay {
     output:
         path "cowsay-*"
 
+    script:
     """
     cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file}
     """
diff --git a/hello-nextflow/containers/solutions/hello-containers-4.1.nf b/hello-nextflow/containers/solutions/hello-containers-4.1.nf
index b9f06e1cf0..fc2e9ba7f7 100644
--- a/hello-nextflow/containers/solutions/hello-containers-4.1.nf
+++ b/hello-nextflow/containers/solutions/hello-containers-4.1.nf
@@ -43,6 +43,7 @@ process cowSay {
     output:
         path "cowsay-*"
 
+    script:
     """
     cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file}
     """
diff --git a/hello-nextflow/containers/solutions/hello-containers-4.2.nf b/hello-nextflow/containers/solutions/hello-containers-4.2.nf
index 71a375336a..9a38316c8c 100644
--- a/hello-nextflow/containers/solutions/hello-containers-4.2.nf
+++ b/hello-nextflow/containers/solutions/hello-containers-4.2.nf
@@ -44,6 +44,7 @@ process cowSay {
     output:
         path "cowsay-*"
 
+    script:
     """
     cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file}
     """
diff --git a/hello-nextflow/hello-config/main.nf b/hello-nextflow/hello-config/main.nf
index 1956a5392a..c738a07484 100644
--- a/hello-nextflow/hello-config/main.nf
+++ b/hello-nextflow/hello-config/main.nf
@@ -31,6 +31,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/hello-containers.nf b/hello-nextflow/hello-containers.nf
index 951ee93d4f..fa799b78b5 100644
--- a/hello-nextflow/hello-containers.nf
+++ b/hello-nextflow/hello-containers.nf
@@ -42,6 +42,7 @@ process cowSay {
     output:
         path "cowsay-*"
 
+    script:
     """
     cowsay -c "$params.character" -t "\$(cat $input_file)" > cowsay-${input_file}
     """
diff --git a/hello-nextflow/hello-genomics.nf b/hello-nextflow/hello-genomics.nf
index be0ee19c6b..211c97165d 100755
--- a/hello-nextflow/hello-genomics.nf
+++ b/hello-nextflow/hello-genomics.nf
@@ -19,6 +19,7 @@ process SAMTOOLS_INDEX {
 
     output:
 
+    script:
     """
 
     """
diff --git a/hello-nextflow/hello-modules/main.nf b/hello-nextflow/hello-modules/main.nf
index 5570b532f1..ddbd345a95 100644
--- a/hello-nextflow/hello-modules/main.nf
+++ b/hello-nextflow/hello-modules/main.nf
@@ -16,6 +16,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -42,6 +43,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf b/hello-nextflow/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf
index 9475cd33b8..04748f765c 100644
--- a/hello-nextflow/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf
+++ b/hello-nextflow/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf
@@ -21,6 +21,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/hello-nf-test/modules/local/samtools/index/main.nf b/hello-nextflow/hello-nf-test/modules/local/samtools/index/main.nf
index 5117b5d9b3..2f5d92227d 100644
--- a/hello-nextflow/hello-nf-test/modules/local/samtools/index/main.nf
+++ b/hello-nextflow/hello-nf-test/modules/local/samtools/index/main.nf
@@ -16,6 +16,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
diff --git a/hello-nextflow/hello-operators.nf b/hello-nextflow/hello-operators.nf
index 646b7d4ebb..f1c5338c92 100644
--- a/hello-nextflow/hello-operators.nf
+++ b/hello-nextflow/hello-operators.nf
@@ -28,6 +28,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -53,6 +54,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.vcf"     , emit: vcf
         path "${input_bam}.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/hello-world.nf b/hello-nextflow/hello-world.nf
index 4abd41782f..53ee46f851 100755
--- a/hello-nextflow/hello-world.nf
+++ b/hello-nextflow/hello-world.nf
@@ -8,6 +8,7 @@ process sayHello {
     output:
         stdout
 
+    script:
     """
     echo 'Hello World!'
     """
diff --git a/hello-nextflow/solutions/hello-config/final-main.nf b/hello-nextflow/solutions/hello-config/final-main.nf
index 5570b532f1..5179779e19 100644
--- a/hello-nextflow/solutions/hello-config/final-main.nf
+++ b/hello-nextflow/solutions/hello-config/final-main.nf
@@ -15,7 +15,8 @@ process SAMTOOLS_INDEX {
 
     output:
         tuple path(input_bam), path("${input_bam}.bai")
-
+    
+    script:
     """
     samtools index '$input_bam'
     """
@@ -42,6 +43,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf
index 138ab8f479..7d99154343 100644
--- a/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf
+++ b/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf
@@ -22,6 +22,7 @@ process SAMTOOLS_INDEX {
     output:
         path "${input_bam}.bai"
 
+    script:
     """
     samtools index '$input_bam'
     """
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf
index c668b742e1..6e1ef58d92 100644
--- a/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf
+++ b/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf
@@ -28,6 +28,7 @@ process SAMTOOLS_INDEX {
     output:
         path "${input_bam}.bai"
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -54,6 +55,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.vcf"     , emit: vcf
         path "${input_bam}.vcf.idx" , emit: idx 
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf
index 5f42ec999e..29fe157853 100644
--- a/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf
+++ b/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf
@@ -32,6 +32,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -57,6 +58,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.vcf"     , emit: vcf
         path "${input_bam}.vcf.idx" , emit: idx 
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf
index 099a89003e..c0cb837e6d 100644
--- a/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf
+++ b/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf
@@ -28,6 +28,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -53,6 +54,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.vcf"     , emit: vcf
         path "${input_bam}.vcf.idx" , emit: idx 
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-modules/modules/local/gatk/GATK_HAPLOTYPECALLER/main.nf b/hello-nextflow/solutions/hello-modules/modules/local/gatk/haplotypecaller/main.nf
similarity index 98%
rename from hello-nextflow/solutions/hello-modules/modules/local/gatk/GATK_HAPLOTYPECALLER/main.nf
rename to hello-nextflow/solutions/hello-modules/modules/local/gatk/haplotypecaller/main.nf
index 9475cd33b8..04748f765c 100644
--- a/hello-nextflow/solutions/hello-modules/modules/local/gatk/GATK_HAPLOTYPECALLER/main.nf
+++ b/hello-nextflow/solutions/hello-modules/modules/local/gatk/haplotypecaller/main.nf
@@ -21,6 +21,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-modules/modules/local/gatk/GATK_JOINTGENOTYPING/main.nf b/hello-nextflow/solutions/hello-modules/modules/local/gatk/jointgenotyping/main.nf
similarity index 100%
rename from hello-nextflow/solutions/hello-modules/modules/local/gatk/GATK_JOINTGENOTYPING/main.nf
rename to hello-nextflow/solutions/hello-modules/modules/local/gatk/jointgenotyping/main.nf
diff --git a/hello-nextflow/solutions/hello-modules/modules/local/samtools/index/main.nf b/hello-nextflow/solutions/hello-modules/modules/local/samtools/index/main.nf
index 5117b5d9b3..2f5d92227d 100644
--- a/hello-nextflow/solutions/hello-modules/modules/local/samtools/index/main.nf
+++ b/hello-nextflow/solutions/hello-modules/modules/local/samtools/index/main.nf
@@ -16,6 +16,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf
index 6d57951254..e264cfdb56 100644
--- a/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf
+++ b/hello-nextflow/solutions/hello-nf-test/modules/local/gatk/haplotypecaller/main.nf
@@ -21,6 +21,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx 
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/main.nf b/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/main.nf
index 5117b5d9b3..2f5d92227d 100644
--- a/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/main.nf
+++ b/hello-nextflow/solutions/hello-nf-test/modules/local/samtools/index/main.nf
@@ -16,6 +16,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-1.nf b/hello-nextflow/solutions/hello-operators/hello-operators-1.nf
index c03c2480cd..c557728926 100644
--- a/hello-nextflow/solutions/hello-operators/hello-operators-1.nf
+++ b/hello-nextflow/solutions/hello-operators/hello-operators-1.nf
@@ -28,6 +28,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -53,6 +54,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx 
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-2.nf b/hello-nextflow/solutions/hello-operators/hello-operators-2.nf
index 4e4aa47ede..fa6574aba7 100644
--- a/hello-nextflow/solutions/hello-operators/hello-operators-2.nf
+++ b/hello-nextflow/solutions/hello-operators/hello-operators-2.nf
@@ -31,6 +31,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx 
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-3.nf b/hello-nextflow/solutions/hello-operators/hello-operators-3.nf
index 6d114bb01e..7175c13f92 100644
--- a/hello-nextflow/solutions/hello-operators/hello-operators-3.nf
+++ b/hello-nextflow/solutions/hello-operators/hello-operators-3.nf
@@ -31,6 +31,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
     """
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
         path "${input_bam}.g.vcf"     , emit: vcf
         path "${input_bam}.g.vcf.idx" , emit: idx 
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-world/hello-world-1.nf b/hello-nextflow/solutions/hello-world/hello-world-1.nf
index e1406c8537..a67f1016cc 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-1.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-1.nf
@@ -5,6 +5,7 @@ process sayHello {
     output:
         stdout
 
+    script:
     """
     echo 'Hello World!'
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-2.nf b/hello-nextflow/solutions/hello-world/hello-world-2.nf
index 4abd41782f..53ee46f851 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-2.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-2.nf
@@ -8,6 +8,7 @@ process sayHello {
     output:
         stdout
 
+    script:
     """
     echo 'Hello World!'
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-3.nf b/hello-nextflow/solutions/hello-world/hello-world-3.nf
index 2fd13df07c..026a593a83 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-3.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-3.nf
@@ -10,6 +10,7 @@ process sayHello {
     output:
         path 'output.txt'
 
+    script:
     """
     echo 'Hello World!' > output.txt
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-4.nf b/hello-nextflow/solutions/hello-world/hello-world-4.nf
index 2fd13df07c..026a593a83 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-4.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-4.nf
@@ -10,6 +10,7 @@ process sayHello {
     output:
         path 'output.txt'
 
+    script:
     """
     echo 'Hello World!' > output.txt
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-5.nf b/hello-nextflow/solutions/hello-world/hello-world-5.nf
index d5c435ec42..7d7720960b 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-5.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-5.nf
@@ -13,6 +13,7 @@ process sayHello {
     output:
         path "output.txt"
 
+    script:
     """
     echo '$greeting' > output.txt
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-6.nf b/hello-nextflow/solutions/hello-world/hello-world-6.nf
index 3f6ab61267..42350793a1 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-6.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-6.nf
@@ -18,6 +18,7 @@ process sayHello {
     output:
         path "output.txt"
 
+    script:
     """
     echo '$greeting' > "output.txt"
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-7.nf b/hello-nextflow/solutions/hello-world/hello-world-7.nf
index 8cd4522de7..401dc4ff9f 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-7.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-7.nf
@@ -18,6 +18,7 @@ process sayHello {
     output:
         path "output.txt"
 
+    script:
     """
     echo '$greeting' > "output.txt"
     """
@@ -33,6 +34,7 @@ process convertToUpper {
     output:
         path "UPPER-${input_file}"
 
+    script:
     """
     cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-8.nf b/hello-nextflow/solutions/hello-world/hello-world-8.nf
index a8d71414a8..5b7eba63c0 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-8.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-8.nf
@@ -18,6 +18,7 @@ process sayHello {
     output:
         path "${greeting}-output.txt"
 
+    script:
     """
     echo '$greeting' > '$greeting-output.txt'
     """
@@ -33,6 +34,7 @@ process convertToUpper {
     output:
         path "UPPER-${input_file}"
 
+    script:
     """
     cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
     """
diff --git a/hello-nextflow/solutions/hello-world/hello-world-9.nf b/hello-nextflow/solutions/hello-world/hello-world-9.nf
index d0fba4d99a..22bcb5f078 100755
--- a/hello-nextflow/solutions/hello-world/hello-world-9.nf
+++ b/hello-nextflow/solutions/hello-world/hello-world-9.nf
@@ -18,6 +18,7 @@ process sayHello {
     output:
         path "${greeting}-output.txt"
 
+    script:
     """
     echo '$greeting' > '$greeting-output.txt'
     """
@@ -36,6 +37,7 @@ process convertToUpper {
     output:
         path "UPPER-${input_file}"
 
+    script:
     """
     cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
     """
diff --git a/troubleshoot/exercise1/hello-gatk.nf b/troubleshoot/exercise1/hello-gatk.nf
index 333fd0785e..e7a0d8af99 100755
--- a/troubleshoot/exercise1/hello-gatk.nf
+++ b/troubleshoot/exercise1/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
 
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
     output:
         tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
@@ -85,6 +87,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf"
         path "${cohort_name}.joint.vcf.idx"
 
+    script:
     """
     gatk GenomicsDBImport \
         --sample-name-map ${sample_map} \
diff --git a/troubleshoot/exercise2/hello-gatk.nf b/troubleshoot/exercise2/hello-gatk.nf
index b60d2af578..787de90077 100755
--- a/troubleshoot/exercise2/hello-gatk.nf
+++ b/troubleshoot/exercise2/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
 
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
     output:
         tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
@@ -85,6 +87,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf"
         path "${cohort_name}.joint.vcf.idx"
 
+    script:
     """
     gatk GenomicsDBImport \
         --sample-name-map ${sample_map} \
diff --git a/troubleshoot/exercise3/hello-gatk.nf b/troubleshoot/exercise3/hello-gatk.nf
index 3ed46f8efe..f243458a17 100755
--- a/troubleshoot/exercise3/hello-gatk.nf
+++ b/troubleshoot/exercise3/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
 
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
     output:
         tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
@@ -85,6 +87,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf"
         path "${cohort_name}.joint.vcf.idx"
 
+    script:
     """
     gatk GenomicsDBImport \
         --sample-name-map ${sample_map} \
diff --git a/troubleshoot/exercise4/hello-gatk.nf b/troubleshoot/exercise4/hello-gatk.nf
index 82cdb857b3..507f388dfa 100755
--- a/troubleshoot/exercise4/hello-gatk.nf
+++ b/troubleshoot/exercise4/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
 
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
     output:
         tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
@@ -85,6 +87,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf"
         path "${cohort_name}.joint.vcf.idx"
 
+    script:
     """
     gatk GenomicsDBImport \
         --sample-name-map ${sample_map} \
diff --git a/troubleshoot/exercise5/hello-gatk.nf b/troubleshoot/exercise5/hello-gatk.nf
index 19544e43f8..4277c37913 100755
--- a/troubleshoot/exercise5/hello-gatk.nf
+++ b/troubleshoot/exercise5/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
 
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
     output:
         tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
@@ -85,6 +87,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf"
         path "${cohort_name}.joint.vcf.idx"
 
+    script:
     """
     gatk GenomicsDBImport \
         --sample-name-map ${sample_map} \
diff --git a/troubleshoot/exercise6/hello-gatk.nf b/troubleshoot/exercise6/hello-gatk.nf
index 83446096dd..cdae1936d9 100755
--- a/troubleshoot/exercise6/hello-gatk.nf
+++ b/troubleshoot/exercise6/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
 
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
     output:
         tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
@@ -85,6 +87,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf"
         path "${cohort_name}.joint.vcf.idx"
 
+    script:
     """
     gatk GenomicsDBImport \
         --sample-name-map ${sample_map} \
diff --git a/troubleshoot/hello-gatk.nf b/troubleshoot/hello-gatk.nf
index 333fd0785e..e7a0d8af99 100755
--- a/troubleshoot/hello-gatk.nf
+++ b/troubleshoot/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${input_bam}.bai")
 
+    script:
     """
     samtools index '$input_bam'
 
@@ -56,6 +57,7 @@ process GATK_HAPLOTYPECALLER {
     output:
         tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")
 
+    script:
     """
     gatk HaplotypeCaller \
         -R ${ref_fasta} \
@@ -85,6 +87,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf"
         path "${cohort_name}.joint.vcf.idx"
 
+    script:
     """
     gatk GenomicsDBImport \
         --sample-name-map ${sample_map} \