Add script:

Author: pinin4fjords

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'
     """

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} \

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} \

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} \

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} \

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} \

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} \

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'
     """

hello-nextflow/solutions/hello-modules/modules/local/gatk/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} \

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'
     """