Merge branch 'main' of https://github.com/fhdsl/WDL_Workflows_Guide into main

Author: jhudsl-robot

01-intro.Rmd

@@ -8,7 +8,7 @@ ottrpal::set_knitr_image_path()
 
 Welcome to building your first WDL workflow! This guide will help you strategically develop and scale up a WDL workflow that is iterative, reproducible, and efficient in terms of time and resource used.
 
-To make sure that we are on the same page, this guide assumes that you are able to run a WDL on a computing engine of your choice, such as Cromwell, miniWDL, or a cloud computing environment such as Terra, AnVIL, or Dockstore. This guide also assumes that you have a beginner's understanding of the WDL syntax, and we will link out to additional resources to fill in the knowledge gap as needed! If you have never seen the WDL language in action, a great place to start is [OpenWDL docs](https://docs.openwdl.org/en/stable/) -- it teaches you the basic syntax and showcases WDL features via concrete examples.
+To make sure that we are on the same page, this guide assumes that you are able to run a WDL on a computing engine of your choice, such as Cromwell, miniwdl, or a cloud computing environment such as Terra, AnVIL, or Dockstore. This guide also assumes that you have a beginner's understanding of the WDL syntax, and we will link out to additional resources to fill in the knowledge gap as needed! If you have never seen the WDL language in action, a great place to start is [OpenWDL docs](https://docs.openwdl.org/en/stable/) -- it teaches you the basic syntax and showcases WDL features via concrete examples.
 
 ## Review of basic WDL syntax
 

02-workflow-plan.Rmd

@@ -49,7 +49,7 @@ To serve as an example we use here whole exome sequencing data from three cell l
 HCC4006 is a lung cancer cell line that has a mutation in the gene *EGFR* (Epithelial Growth Factor Receptor) a proto-oncogene. Mutations in *EGFR* result in the abnormal constitutive activation of the EGFR signaling pathway and drive cancer. In this cell-line specifically the *EGFR* mutation is an in-frame deletion in Exon 19. This mutation results in the constitutive activation of the EGFR protein and is therefore oncogenic. 
 
 ### Tumor 2 : CALU1
-CALU1 is a lung cancer cell line that has a mutation in the gene *KRAS* (Kirsten rat sarcoma viral oncogene homolog) . *KRAS* is also a proto-oncogene and the most common cancer-causing mutations lock the protien in an active conformation. Constitutive activation of *KRAS* results in  carcinogenesis. In this cell-line *KRAS*  has a point/missense mutation resulting in the substitution of the amino acid glycine (G) with cysteine (C) at position 12 of the KRAS protein (commonly known as the KRAS G12C mutation). This mutation results in the constitutive activation of KRAS and drives carcinogenesis. 
+CALU1 is a lung cancer cell line that has a mutation in the gene *KRAS* (Kirsten rat sarcoma viral oncogene homolog) . *KRAS* is also a proto-oncogene and the most common cancer-causing mutations lock the protein in an active conformation. Constitutive activation of *KRAS* results in  carcinogenesis. In this cell-line *KRAS*  has a point/missense mutation resulting in the substitution of the amino acid glycine (G) with cysteine (C) at position 12 of the KRAS protein (commonly known as the KRAS G12C mutation). This mutation results in the constitutive activation of KRAS and drives carcinogenesis. 
 
 ### Normal : MOLM13
 MOLM 13 is a human leukemia cell line commonly used in research. While it is also a cancer cell line for the purposes of this workflow example we are going to consider it as a "normal". This cell line does not have mutations in *EGFR* nor in *KRAS* and therefore is a practical surrogate in lieu of a conventional normal sample

03-first-task.Rmd

@@ -157,7 +157,7 @@ For many programs, an input file being at `./ref.fa` versus `/_miniwdl_inputs/0/
 <details>
 <summary><b>Another example of file localization issue.</b></summary>
 
-bwa is not the only program that makes assumptions about where files are located, and assumptions being made do not only affect reference genome files. Bioinformatics programs that take in some sort of index file requently assume that index file is located in the same directory as the non-index input. For example, if you were to pass in `SAMN1234.bam` into [covstats](https://github.com/brentp/goleft/tree/master/covstats), it would expect an index file named `SAMN1234.bam.bai` or `SAMN1234.bai` in the same directory as the bam file, [as seen in the source code here](https://github.com/brentp/goleft/blob/fa6b00d20d1f73a068ffbab49a5769d173cae56d/covstats/covstats.go#L239). As there is no way to specify that the index file manually, you need to take that into consideration when writing WDLs involving covstats, bwa, and other similar tools.
+bwa is not the only program that makes assumptions about where files are located, and assumptions being made do not only affect reference genome files. Bioinformatics programs that take in some sort of index file frequently assume that index file is located in the same directory as the non-index input. For example, if you were to pass in `SAMN1234.bam` into [covstats](https://github.com/brentp/goleft/tree/master/covstats), it would expect an index file named `SAMN1234.bam.bai` or `SAMN1234.bai` in the same directory as the bam file, [as seen in the source code here](https://github.com/brentp/goleft/blob/fa6b00d20d1f73a068ffbab49a5769d173cae56d/covstats/covstats.go#L239). As there is no way to specify that the index file manually, you need to take that into consideration when writing WDLs involving covstats, bwa, and other similar tools.
 
 </details>
 
@@ -308,7 +308,7 @@ WDL is built to make use of Docker as it makes handling software dependencies mu
 
 * You may not have permission to install software if you are using an institute HPC or other shared resource
 
-When you run a WDL task that has a `docker` runtime attribute, your task will be executed in a Docker container sandbox environment. This container sandbox is derived from a template called a Docker image, which packages installed software in a special filesystem. This is one of the main features of a Docker image -- because a Docker image packages the software you need, you can skip much of the installation and dependency issues associated with using new software, and because you take actions within a Docker container sandbox, it's unlikely for you to "mess up" your main system's files. Although a Docker container is, strictly speaking, not the same as a virtual machine, it is helpful to think of it as one if you are new to Docker. Docker containers are managed by Docker Engine, and the official Docker GUI is called Docker Desktop.
+When you run a WDL task that has a `docker` runtime attribute, your task will be executed in a Docker container sandbox environment. This container sandbox is derived from a template called a Docker image, which packages installed software in a special file system. This is one of the main features of a Docker image -- because a Docker image packages the software you need, you can skip much of the installation and dependency issues associated with using new software, and because you take actions within a Docker container sandbox, it's unlikely for you to "mess up" your main system's files. Although a Docker container is, strictly speaking, not the same as a virtual machine, it is helpful to think of it as one if you are new to Docker. Docker containers are managed by Docker Engine, and the official Docker GUI is called Docker Desktop.
 
 <details>
 <summary><b>More information on finding and developing Docker images. </b></summary>

06-arrays.Rmd

@@ -17,7 +17,7 @@ In this chapter, we'll be going over:
 - How arrays differ from Structs
 
 ## The array type
-Arrays are essentially lists of another [primitive type](https://en.wikipedia.org/wiki/Primitive_data_type). It is most common to see Array[File] in WDLs, but an array can contain integers, floats, strings, and the like. An array can only have one of a given primative type. For example, an Array[String] could contain the strings "cat" and "dog" but not the integer 1965 (however, it could have "1965" as a string).
+Arrays are essentially lists of another [primitive type](https://en.wikipedia.org/wiki/Primitive_data_type). It is most common to see Array[File] in WDLs, but an array can contain integers, floats, strings, and the like. An array can only have one of a given primitive type. For example, an Array[String] could contain the strings "cat" and "dog" but not the integer 1965 (however, it could have "1965" as a string).
 
 In chapter 4, we went over the struct data type and used it to handle a myriad of reference genome files. Arrays differ from structs in that arrays are numerically indexed, which means that a member of the array can be accessed by its position in the array. On the other hand, each variable within a struct has its own name, and you use that name to reference it rather than a numerical index.
 

09-appendix-backends.Rmd

@@ -3,7 +3,7 @@ ottrpal::set_knitr_image_path()
 ```
 
 # Appendix: Backends and Executors
-Generally speaking, WDL workflows are quite portable thanks to their usage of Docker images to maintain software depenendencies. However, the executor used to run WDLs and what backend they are being run upon can lead to specific scenarios where minor tweaks to your WDL are necessary to ensure portability.
+Generally speaking, WDL workflows are quite portable thanks to their usage of Docker images to maintain software dependencies. However, the executor used to run WDLs and what backend they are being run upon can lead to specific scenarios where minor tweaks to your WDL are necessary to ensure portability.
 
 ## Commonly used runtime attributes
 Runtime attributes do not behave the same on all platforms. Here are how some of the most commonly used runtime attributes work on some of the most common WDL setups.
@@ -36,7 +36,7 @@ Other notes:
 
 * If you just want to check workflows are valid, you can run `womtool` as a jar file (available on Cromwell's GitHub page). This will check not only the WDL file you pass it, but also any WDLs it imports.
 
-* Cromwell does not use call cacheing on most backends, but it is the default on Terra. For non-Terra backends, it can be enabled in the Cromwell configuration file.
+* Cromwell does not use call caching on most backends, but it is the default on Terra. For non-Terra backends, it can be enabled in the Cromwell configuration file.
 
 * Cromwell supports the `gpu` and `disks` runtime attributes on certain backends. If using the `gpu` runtime attribute, make sure your task is set up correctly to properly use this resource.
 
@@ -51,7 +51,7 @@ Other notes:
 
 * miniwdl's equivalent to `womtool` is `miniwdl check`, but it also includes `shellcheck` to check the command section of your tasks.
 
-* miniwdl supports call cacheing, but it is turned off by default.
+* miniwdl supports call caching, but it is turned off by default.
 
 * miniwdl does not support the `gpu` or `disks` runtime attributes and will ignore them if present in a task's runtime section.
 

docs/01-intro.md

@@ -6,7 +6,7 @@
 
 Welcome to building your first WDL workflow! This guide will help you strategically develop and scale up a WDL workflow that is iterative, reproducible, and efficient in terms of time and resource used.
 
-To make sure that we are on the same page, this guide assumes that you are able to run a WDL on a computing engine of your choice, such as Cromwell, miniWDL, or a cloud computing environment such as Terra, AnVIL, or Dockstore. This guide also assumes that you have a beginner's understanding of the WDL syntax, and we will link out to additional resources to fill in the knowledge gap as needed! If you have never seen the WDL language in action, a great place to start is [OpenWDL docs](https://docs.openwdl.org/en/stable/) -- it teaches you the basic syntax and showcases WDL features via concrete examples.
+To make sure that we are on the same page, this guide assumes that you are able to run a WDL on a computing engine of your choice, such as Cromwell, miniwdl, or a cloud computing environment such as Terra, AnVIL, or Dockstore. This guide also assumes that you have a beginner's understanding of the WDL syntax, and we will link out to additional resources to fill in the knowledge gap as needed! If you have never seen the WDL language in action, a great place to start is [OpenWDL docs](https://docs.openwdl.org/en/stable/) -- it teaches you the basic syntax and showcases WDL features via concrete examples.
 
 ## Review of basic WDL syntax
 

docs/02-workflow-plan.md

@@ -47,7 +47,7 @@ To serve as an example we use here whole exome sequencing data from three cell l
 HCC4006 is a lung cancer cell line that has a mutation in the gene *EGFR* (Epithelial Growth Factor Receptor) a proto-oncogene. Mutations in *EGFR* result in the abnormal constitutive activation of the EGFR signaling pathway and drive cancer. In this cell-line specifically the *EGFR* mutation is an in-frame deletion in Exon 19. This mutation results in the constitutive activation of the EGFR protein and is therefore oncogenic. 
 
 ### Tumor 2 : CALU1
-CALU1 is a lung cancer cell line that has a mutation in the gene *KRAS* (Kirsten rat sarcoma viral oncogene homolog) . *KRAS* is also a proto-oncogene and the most common cancer-causing mutations lock the protien in an active conformation. Constitutive activation of *KRAS* results in  carcinogenesis. In this cell-line *KRAS*  has a point/missense mutation resulting in the substitution of the amino acid glycine (G) with cysteine (C) at position 12 of the KRAS protein (commonly known as the KRAS G12C mutation). This mutation results in the constitutive activation of KRAS and drives carcinogenesis. 
+CALU1 is a lung cancer cell line that has a mutation in the gene *KRAS* (Kirsten rat sarcoma viral oncogene homolog) . *KRAS* is also a proto-oncogene and the most common cancer-causing mutations lock the protein in an active conformation. Constitutive activation of *KRAS* results in  carcinogenesis. In this cell-line *KRAS*  has a point/missense mutation resulting in the substitution of the amino acid glycine (G) with cysteine (C) at position 12 of the KRAS protein (commonly known as the KRAS G12C mutation). This mutation results in the constitutive activation of KRAS and drives carcinogenesis. 
 
 ### Normal : MOLM13
 MOLM 13 is a human leukemia cell line commonly used in research. While it is also a cancer cell line for the purposes of this workflow example we are going to consider it as a "normal". This cell line does not have mutations in *EGFR* nor in *KRAS* and therefore is a practical surrogate in lieu of a conventional normal sample

docs/03-first-task.md

@@ -155,7 +155,7 @@ For many programs, an input file being at `./ref.fa` versus `/_miniwdl_inputs/0/
 <details>
 <summary><b>Another example of file localization issue.</b></summary>
 
-bwa is not the only program that makes assumptions about where files are located, and assumptions being made do not only affect reference genome files. Bioinformatics programs that take in some sort of index file requently assume that index file is located in the same directory as the non-index input. For example, if you were to pass in `SAMN1234.bam` into [covstats](https://github.com/brentp/goleft/tree/master/covstats), it would expect an index file named `SAMN1234.bam.bai` or `SAMN1234.bai` in the same directory as the bam file, [as seen in the source code here](https://github.com/brentp/goleft/blob/fa6b00d20d1f73a068ffbab49a5769d173cae56d/covstats/covstats.go#L239). As there is no way to specify that the index file manually, you need to take that into consideration when writing WDLs involving covstats, bwa, and other similar tools.
+bwa is not the only program that makes assumptions about where files are located, and assumptions being made do not only affect reference genome files. Bioinformatics programs that take in some sort of index file frequently assume that index file is located in the same directory as the non-index input. For example, if you were to pass in `SAMN1234.bam` into [covstats](https://github.com/brentp/goleft/tree/master/covstats), it would expect an index file named `SAMN1234.bam.bai` or `SAMN1234.bai` in the same directory as the bam file, [as seen in the source code here](https://github.com/brentp/goleft/blob/fa6b00d20d1f73a068ffbab49a5769d173cae56d/covstats/covstats.go#L239). As there is no way to specify that the index file manually, you need to take that into consideration when writing WDLs involving covstats, bwa, and other similar tools.
 
 </details>
 
@@ -306,7 +306,7 @@ WDL is built to make use of Docker as it makes handling software dependencies mu
 
 * You may not have permission to install software if you are using an institute HPC or other shared resource
 
-When you run a WDL task that has a `docker` runtime attribute, your task will be executed in a Docker container sandbox environment. This container sandbox is derived from a template called a Docker image, which packages installed software in a special filesystem. This is one of the main features of a Docker image -- because a Docker image packages the software you need, you can skip much of the installation and dependency issues associated with using new software, and because you take actions within a Docker container sandbox, it's unlikely for you to "mess up" your main system's files. Although a Docker container is, strictly speaking, not the same as a virtual machine, it is helpful to think of it as one if you are new to Docker. Docker containers are managed by Docker Engine, and the official Docker GUI is called Docker Desktop.
+When you run a WDL task that has a `docker` runtime attribute, your task will be executed in a Docker container sandbox environment. This container sandbox is derived from a template called a Docker image, which packages installed software in a special file system. This is one of the main features of a Docker image -- because a Docker image packages the software you need, you can skip much of the installation and dependency issues associated with using new software, and because you take actions within a Docker container sandbox, it's unlikely for you to "mess up" your main system's files. Although a Docker container is, strictly speaking, not the same as a virtual machine, it is helpful to think of it as one if you are new to Docker. Docker containers are managed by Docker Engine, and the official Docker GUI is called Docker Desktop.
 
 <details>
 <summary><b>More information on finding and developing Docker images. </b></summary>