Making comments in code consistent; added a table showing the workflo…

…w in `02-workflow-plan.Rmd`
fhdsl · Mar 15, 2024 · 5d37756 · 5d37756
1 parent 51b5774
commit 5d37756
Show file tree

Hide file tree

Showing 5 changed files with 25 additions and 22 deletions.
diff --git a/01-intro.Rmd b/01-intro.Rmd
@@ -111,7 +111,7 @@ task do_something {
         head ~{fastq} >> output.txt
     >>>
     output {
-        File first_ten_lines = "output.txt"  #output variable for task
+        File first_ten_lines = "output.txt"  ## output variable for task
     }
 }
 
@@ -129,7 +129,7 @@ workflow my_workflow {
     }
     
     output {
-        File ten_lines = do_something.first_ten_lines #referring to task output here
+        File ten_lines = do_something.first_ten_lines ## referring to task output here
     }
 }
 ```

diff --git a/02-workflow-plan.Rmd b/02-workflow-plan.Rmd
@@ -17,11 +17,14 @@ The workflow diagram:
 
 The tasks involved:
 
-1.  `BwaMem` aligns the samples to the reference genome (hg19). (outputs a `.bam` file)
-2.  `MarkDuplicates` marks PCR duplicates. (outputs a `.bam` file)
-3.  `ApplyBaseRecalibrator` perform base quality recalibration. (outputs a `.bam` file)
-4.  `Mutect2` performs paired somatic mutation calling. (outputs a `.vcf` file)
-5.  `annovar` annotates the called somatic mutations. (outputs a `.vcf` file)
+|Task|Function|Inputs|Outputs|
+|----|--------|------|-------|
+|`BwaMem`|aligns the samples to the reference genome (hg19)|FASTA (`.fa`) file|`.bam` file|
+|`MarkDuplicates|marks PCR duplicates|`.bam` file|marked `.bam` file|
+|`ApplyBaseRecalibrator`|performs base quality recalibration|marked `.bam` file|`.bam` file|
+|`Mutect2`|performs paired somatic mutation calling|`.bam` file|`.vcf` file|
+|`annovar`|annotates the called somatic mutations|`.vcf` file with somatic mutations|annotated `.vcf` file| 
+
 
 ## Workflow testing strategy
 

diff --git a/03-first-task.Rmd b/03-first-task.Rmd
@@ -235,7 +235,7 @@ task BwaMem {
   String read_group_id = "ID:" + base_file_name
   String sample_name = "SM:" + base_file_name
   String platform = "illumina"
-  String platform_info = "PL:" + platform   # Create the platform information
+  String platform_info = "PL:" + platform   ## Create the platform information
 
   command <<<
     set -eo pipefail

diff --git a/04-linear-chain.Rmd b/04-linear-chain.Rmd
@@ -298,7 +298,7 @@ task BwaMem {
   String read_group_id = "ID:" + base_file_name
   String sample_name = "SM:" + base_file_name
   String platform = "illumina"
-  String platform_info = "PL:" + platform   # Create the platform information
+  String platform_info = "PL:" + platform   ## Create the platform information
 
 
   command <<<
@@ -331,7 +331,7 @@ task BwaMem {
   }
 }
 
-# Mark duplicates
+## Mark duplicates
 task MarkDuplicates {
   input {
     File input_bam
@@ -415,7 +415,7 @@ task ApplyBaseRecalibrator {
       -R ~{ref_fasta_local} \
       
 
-  #finds the current sort order of this bam file
+  ## finds the current sort order of this bam file
   samtools view -H ~{base_file_name}.recal.bam | grep @SQ | sed 's/@SQ\tSN:\|LN://g' > ~{base_file_name}.sortOrder.txt
 >>>
 

diff --git a/05-structs.Rmd b/05-structs.Rmd
@@ -26,14 +26,14 @@ struct referenceGenome {
 workflow minidata_mutation_calling_v1 {
   input {
     File sampleFastq
-    referenceGenome refGenome
+    referenceGenome refGenome           ## our struct
     ...
   }
-  # Map reads to reference
+  ## Map reads to reference
   call BwaMem {
     input:
       input_fastq = sampleFastq,
-      refGenome = refGenome
+      refGenome = refGenome             ## our struct 
   }
 }
 ```
@@ -81,13 +81,13 @@ task BwaMem {
   String read_group_id = "ID:" + base_file_name
   String sample_name = "SM:" + base_file_name
   String platform = "illumina"
-  String platform_info = "PL:" + platform   # Create the platform information
+  String platform_info = "PL:" + platform   ## Create the platform information
 
 
   command <<<
     set -eo pipefail
 
-    #can we iterate through a struct??
+    ## can we iterate through a struct??
     mv ~{refGenome.ref_fasta} .
     mv ~{refGenome.ref_fasta_index} .
     mv ~{refGenome.ref_dict} .
@@ -167,7 +167,7 @@ workflow minidata_mutation_calling_v1 {
   call BwaMem {
     input:
       input_fastq = sampleFastq,
-      refGenome = refGenome
+      refGenome = refGenome       ## our struct
   }
   
   call MarkDuplicates {
@@ -183,7 +183,7 @@ workflow minidata_mutation_calling_v1 {
       dbSNP_vcf_index = dbSNP_vcf_index,
       known_indels_sites_VCFs = known_indels_sites_VCFs,
       known_indels_sites_indices = known_indels_sites_indices,
-      refGenome = refGenome
+      refGenome = refGenome           ## our struct
     }
 
   call Mutect2TumorOnly {
@@ -229,7 +229,7 @@ workflow minidata_mutation_calling_v1 {
 task BwaMem {
   input {
     File input_fastq
-    referenceGenome refGenome
+    referenceGenome refGenome           ## our struct
   }
   
   String base_file_name = basename(input_fastq, ".fastq")
@@ -238,7 +238,7 @@ task BwaMem {
   String read_group_id = "ID:" + base_file_name
   String sample_name = "SM:" + base_file_name
   String platform = "illumina"
-  String platform_info = "PL:" + platform   # Create the platform information
+  String platform_info = "PL:" + platform   ## Create the platform information
 
 
   command <<<
@@ -315,7 +315,7 @@ task ApplyBaseRecalibrator {
     File dbSNP_vcf_index
     File known_indels_sites_VCFs
     File known_indels_sites_indices
-    referenceGenome refGenome
+    referenceGenome refGenome         ## our struct
   }
   
   String base_file_name = basename(input_bam, ".duplicates_marked.bam")
@@ -357,7 +357,7 @@ task ApplyBaseRecalibrator {
       -R ~{ref_fasta_local} \
       
 
-  #finds the current sort order of this bam file
+  # finds the current sort order of this bam file
   samtools view -H ~{base_file_name}.recal.bam | grep @SQ | sed 's/@SQ\tSN:\|LN://g' > ~{base_file_name}.sortOrder.txt
 >>>