nextflow-io · pinin4fjords · Nov 6, 2024 · Nov 6, 2024 · Nov 6, 2024 · Nov 6, 2024
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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-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
@@ -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-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
@@ -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
@@ -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
@@ -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/...s/local/gatk/GATK_HAPLOTYPECALLER/main.nf → ...odules/local/gatk/haplotypecaller/main.nf b/...s/local/gatk/GATK_HAPLOTYPECALLER/main.nf → ...odules/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/...s/local/gatk/GATK_JOINTGENOTYPING/main.nf → ...odules/local/gatk/jointgenotyping/main.nf b/...s/local/gatk/GATK_JOINTGENOTYPING/main.nf → ...odules/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
@@ -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
@@ -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
@@ -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
@@ -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 '$greeting' > "output.txt"
     """
-Original file line number
+Diff line change
@@ Expand Up / @@ -422,6 +422,7 @@ process GATK_GENOMICSDB { @@
         output:
             path "${cohort_name}_gdb"
+        script:
         """
         gatk GenomicsDBImport \
             -V ${all_gvcfs} \
@@ Expand Down @@