script: everywhere

pinin4fjords · pinin4fjords · commit cb49ea72e01a · 2024-11-06T15:48:02.000Z
diff --git 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
@@ -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
@@ -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-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
@@ -19,6 +19,7 @@ process SAMTOOLS_INDEX {
 
     output:
 
+    script:
     """
 
     """
diff --git 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
@@ -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
@@ -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 ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-1.nf
@@ -22,6 +22,7 @@ process SAMTOOLS_INDEX {
     output:
         path "${input_bam}.bai"
 
+    script:
     """
     samtools index '$input_bam'
     """
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-2.nf
@@ -28,6 +28,7 @@ process SAMTOOLS_INDEX {
     output:
         path "${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 ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-3.nf
@@ -32,6 +32,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${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 ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf b/hello-nextflow/solutions/hello-genomics/hello-genomics-4.nf
@@ -28,6 +28,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${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 ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-1.nf b/hello-nextflow/solutions/hello-operators/hello-operators-1.nf
@@ -28,6 +28,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${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 ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-2.nf b/hello-nextflow/solutions/hello-operators/hello-operators-2.nf
@@ -31,6 +31,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${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 ${ref_fasta} \
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-3.nf b/hello-nextflow/solutions/hello-operators/hello-operators-3.nf
@@ -31,6 +31,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple path(input_bam), path("${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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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 ${sample_map} \
diff --git a/troubleshoot/exercise2/hello-gatk.nf b/troubleshoot/exercise2/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${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 ${sample_map} \
diff --git a/troubleshoot/exercise3/hello-gatk.nf b/troubleshoot/exercise3/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${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 ${sample_map} \
diff --git a/troubleshoot/exercise4/hello-gatk.nf b/troubleshoot/exercise4/hello-gatk.nf
@@ -33,6 +33,7 @@ process SAMTOOLS_INDEX {
     output:
         tuple val(id), path(input_bam), path("${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
diff --git a/troubleshoot/exercise6/hello-gatk.nf b/troubleshoot/exercise6/hello-gatk.nf
diff --git a/troubleshoot/hello-gatk.nf b/troubleshoot/hello-gatk.nf

-Original file line number
+Diff line change
     output:
 +    script:
     """
     """