From ba80645809836a94f6a8ef1c4c8d942e66ee1075 Mon Sep 17 00:00:00 2001 From: carriewright11 Date: Wed, 6 Mar 2024 14:40:20 -0500 Subject: [PATCH 1/5] fixing cons formatting --- index.Rmd | 1 + 1 file changed, 1 insertion(+) diff --git a/index.Rmd b/index.Rmd index dfc9f7b..238fada 100644 --- a/index.Rmd +++ b/index.Rmd @@ -40,6 +40,7 @@ WDL has some really helpful advantages compared to other frameworks: ### WDL Cons Of course, nothing is free. WDL does require you to understand the basic concepts and terminologies including: + - Basics of Docker - Understanding the WDL framework - WDLizing your bash scripts into tasks From a772cfc2f13dfb203969234c06e43e470a3fcd2d Mon Sep 17 00:00:00 2001 From: carriewright11 Date: Wed, 6 Mar 2024 14:43:41 -0500 Subject: [PATCH 2/5] breaking down objectives and changing to background --- index.Rmd | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/index.Rmd b/index.Rmd index 238fada..484b5be 100644 --- a/index.Rmd +++ b/index.Rmd @@ -48,8 +48,14 @@ Of course, nothing is free. WDL does require you to understand the basic concept ## Curriculum -The course covers the following: how to write an effective WDL task, link multiple WDL tasks together in a workflow, organize variables via structs, scale multiple samples via Arrays, reuse repeated tasks via task aliasing, and configure settings for the execution engine. +The course covers the following: -## Relevant resources +- How to write an effective WDL task +- Link multiple WDL tasks together in a workflow +- Organize variables via structs, scale multiple samples via Arrays +- Reuse repeated tasks via task aliasing +- Configure settings for the execution engine -An excellent WDL companion resource that is not platform dependent is [OpenWDL Docs](https://docs.openwdl.org/en/stable/). OpenWDL Docs focuses on the basic grammar of WDL as well as providing excellent cookbook recipes of common WDL workflow structures. In this guide we will reference these basic grammar structures and common workflow cookbook recipes. +## Suggested Background + +If you are new to WDL, an excellent WDL companion resource that is not platform dependent is [OpenWDL Docs](https://docs.openwdl.org/en/stable/). OpenWDL Docs focuses on the basic grammar of WDL as well as providing excellent cookbook recipes of common WDL workflow structures. In this guide we will reference these basic grammar structures and common workflow cookbook recipes. From bc6109624026e483a021400e4609e040936c5d90 Mon Sep 17 00:00:00 2001 From: carriewright11 Date: Wed, 6 Mar 2024 14:49:29 -0500 Subject: [PATCH 3/5] moving resources up and adjusting text for readiblity --- index.Rmd | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/index.Rmd b/index.Rmd index 484b5be..8a6ccab 100644 --- a/index.Rmd +++ b/index.Rmd @@ -21,6 +21,10 @@ output: The course is intended for first time developers of the [WDL workflow language](https://github.com/openwdl/wdl), who wants to iteratively develop a WDL bioinformatics workflow. In order to use this guide the audience should be able to comprehend introductory WDL syntax, and should be able to run a WDL workflow on a computing engine of their choice, such as Cromwell, miniWDL, or a cloud computing environment such as Terra, AnVIL, or Dockstore. +### Relevant Resources + +If you are new to WDL, [OpenWDL Docs](https://docs.openwdl.org/en/stable/) is an excellent WDL companion resource to help you get started and is platform agnostic. OpenWDL Docs focuses on the basic grammar of WDL as well as providing excellent cookbook recipes of common WDL workflow structures. In this guide we will reference these basic grammar structures and common workflow cookbook recipes. + ## Why WDL? You may have encountered other workflow tools, such as Snakemake or Nextflow, and those are highly capable. Why learn a brand new workflow language? Let's review some WDL Pros and Cons: @@ -56,6 +60,4 @@ The course covers the following: - Reuse repeated tasks via task aliasing - Configure settings for the execution engine -## Suggested Background -If you are new to WDL, an excellent WDL companion resource that is not platform dependent is [OpenWDL Docs](https://docs.openwdl.org/en/stable/). OpenWDL Docs focuses on the basic grammar of WDL as well as providing excellent cookbook recipes of common WDL workflow structures. In this guide we will reference these basic grammar structures and common workflow cookbook recipes. From 2a190e5865969e7cbd9a30fa2025e24b45587a76 Mon Sep 17 00:00:00 2001 From: carriewright11 Date: Thu, 7 Mar 2024 14:19:43 -0500 Subject: [PATCH 4/5] fixing part of the spelling - leaving some for other chapters to avoid merge conflicts --- index.Rmd | 2 +- resources/dictionary.txt | 52 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+), 1 deletion(-) diff --git a/index.Rmd b/index.Rmd index 8a6ccab..0cd6a4a 100644 --- a/index.Rmd +++ b/index.Rmd @@ -39,7 +39,7 @@ WDL has some really helpful advantages compared to other frameworks: - **Sharing**. A WDL workflow is much easier to share with colleagues and is a good way to get credit for work you do everyday. If you spent time building it, why not share it? WDL is also an open standard and supported by a number of software tools. -- **Running and Making WDL workflows is a transferrable skill.** Genomics and Pharma companies rely on WDL workflows to process thousands of FASTA/VCF files for their studies. They need more experts. It makes you more hireable within both Academia and Industry. +- **Running and Making WDL workflows is a transferable skill.** Genomics and Pharma companies rely on WDL workflows to process thousands of FASTA/VCF files for their studies. They need more experts. It makes you more hireable within both Academia and Industry. ### WDL Cons diff --git a/resources/dictionary.txt b/resources/dictionary.txt index ccb15b9..5bfdd24 100644 --- a/resources/dictionary.txt +++ b/resources/dictionary.txt @@ -12,15 +12,25 @@ BIPOC bizz Bloomberg Bookdown +bootDiskSizeGB +bp +bwa +BwaMem +bwt carcinogenesis +CALU +chapt CLI conda Coursera covstats cpu +creativecommons css +cysteine Datatrail DataTrail +DISCOVERABLE Dockerfile Dockerhub Docker's @@ -28,17 +38,25 @@ DockerException Dockstore DNAnexus dropdown +EGFR enforceability exome +faq favicon +FHDaSL +Funder fyi GATK GDSCN GitHub Github GH +glycine +HCC heredoc hireable +hg +homolog https iframe impactful @@ -46,28 +64,62 @@ ITCR itcrtraining iteratively ITN +KRAS +Laderas Leanpub +Licensor +LICENSOR Markua mentorship +MERCHANTABILITY missense miniwdl +miniWDL miniwdl's +MOLM +Moorthi +multithreading +Muschelli +MuTect +NextFlow NCI NHGRI +O'Farrell +oncogenic +OpenWDL's +OTTR ottrpal +parallely parallelization +Paguirigan Pandoc +Pharma plaintext +png +podman +proto preemptible preemptibles recalibration +recalibrated +repo reproducibility +Savonen scalable +Scalability +socio +sexualized +Sitapriya +Snakemake SSD struct structs +synched UE UE5 +Videographer +Videography +WIPO UI unintuitive underserved From a2c8ca4079d8cbb168426b56a2e6a5828b319a11 Mon Sep 17 00:00:00 2001 From: carriewright11 Date: Thu, 7 Mar 2024 14:24:07 -0500 Subject: [PATCH 5/5] I think ash perfers miniwdl instead of miniWDL - so removing that from the dictionary --- resources/dictionary.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/resources/dictionary.txt b/resources/dictionary.txt index 5bfdd24..29121ee 100644 --- a/resources/dictionary.txt +++ b/resources/dictionary.txt @@ -74,7 +74,6 @@ mentorship MERCHANTABILITY missense miniwdl -miniWDL miniwdl's MOLM Moorthi