diff --git a/docs/hello_nextflow/02_hello_world.md b/docs/hello_nextflow/02_hello_world.md index 4441aa14..64b2fc77 100644 --- a/docs/hello_nextflow/02_hello_world.md +++ b/docs/hello_nextflow/02_hello_world.md @@ -252,17 +252,17 @@ This is the same change we made when we ran the command directly in the terminal _Before:_ ```groovy title="hello-world.nf" linenums="11" -""" -echo 'Hello World!' -""" + """ + echo 'Hello World!' + """ ``` _After:_ ```groovy title="hello-world.nf" linenums="11" -""" -echo 'Hello World!' > output.txt -""" + """ + echo 'Hello World!' > output.txt + """ ``` ### 3.2. Change the output declaration in the `sayHello` process @@ -481,17 +481,17 @@ Now we swap the original hardcoded value for the input variable. _Before:_ ```groovy title="hello-world.nf" linenums="16" -""" -echo 'Hello World!' > output.txt -""" + """ + echo 'Hello World!' > output.txt + """ ``` _After:_ ```groovy title="hello-world.nf" linenums="16" -""" -echo '$greeting' > output.txt -""" + """ + echo '$greeting' > output.txt + """ ``` ### 5.3. Create an input channel diff --git a/docs/hello_nextflow/03_hello_containers.md b/docs/hello_nextflow/03_hello_containers.md index 2e43fdb6..9a885d22 100644 --- a/docs/hello_nextflow/03_hello_containers.md +++ b/docs/hello_nextflow/03_hello_containers.md @@ -431,7 +431,7 @@ For the `quote` container image, you can either use the one you built yourself i A good choice for the `script` block of your getQuote process might be: ```groovy - script: + script: def safe_author = author.tokenize(' ').join('-') """ quote "$author" > quote-${safe_author}.txt diff --git a/docs/hello_nextflow/04_hello_genomics.md b/docs/hello_nextflow/04_hello_genomics.md index 61bc3054..f3ff22e0 100644 --- a/docs/hello_nextflow/04_hello_genomics.md +++ b/docs/hello_nextflow/04_hello_genomics.md @@ -618,16 +618,16 @@ Specifically, where we previously declared two separate input paths in the input _Before:_ ```groovy title="hello-genomics.nf" linenums="49" -input: - path input_bam - path input_bam_index + input: + path input_bam + path input_bam_index ``` _After:_ ```groovy title="hello-genomics.nf" linenums="49" -input: - tuple path(input_bam), path(input_bam_index) + input: + tuple path(input_bam), path(input_bam_index) ``` Of course, since we've now changed the shape of the inputs that `GATK_HAPLOTYPECALLER` expects, we need to update the process call accordingly in the workflow body. diff --git a/docs/hello_nextflow/05_hello_operators.md b/docs/hello_nextflow/05_hello_operators.md index fdaac3c2..f975ea41 100644 --- a/docs/hello_nextflow/05_hello_operators.md +++ b/docs/hello_nextflow/05_hello_operators.md @@ -734,24 +734,24 @@ The second command requires the reference genome files, so we need to add those _Before:_ ```groovy title="hello-operators.nf" linenums="78" -input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name + input: + path all_gvcfs + path all_idxs + path interval_list + val cohort_name ``` _After:_ ```groovy title="hello-operators.nf" linenums="78" -input: - path all_gvcfs - path all_idxs - path interval_list - val cohort_name - path ref_fasta - path ref_index - path ref_dict + input: + path all_gvcfs + path all_idxs + path interval_list + val cohort_name + path ref_fasta + path ref_index + path ref_dict ``` It may seem annoying to type these out, but remember, you only type them once, and then you can run the workflow a million times. Worth it?