Fixes Add indents to match destination of code blocks #422

docs/hello_nextflow/02_hello_world.md

@@ -254,17 +254,17 @@ 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
@@ -483,17 +483,17 @@ 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

docs/hello_nextflow/03_hello_containers.md

@@ -427,7 +427,7 @@ 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

docs/hello_nextflow/04_hello_genomics.md

@@ -628,16 +628,16 @@ 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.

docs/hello_nextflow/05_hello_operators.md

@@ -736,24 +736,24 @@ 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?

docs/hello_nextflow/07_hello_modules.md

@@ -337,7 +337,7 @@ process GATK_JOINTGENOTYPING {
         path "${cohort_name}.joint.vcf.idx" , emit: idx
 
     script:
-        def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ')
+    def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ')
     """
     gatk GenomicsDBImport \
         ${gvcfs_line} \