From 4f98646fa8466819047baf9597dd826d6b318b9b Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 25 Oct 2023 09:37:39 -0700 Subject: [PATCH 1/3] drop unused text (#71) --- .../VariantCalling/gatk-dnaseq-best-practices-workflow.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/dataAnalysis/VariantCalling/gatk-dnaseq-best-practices-workflow.md b/dataAnalysis/VariantCalling/gatk-dnaseq-best-practices-workflow.md index bc32811e..5147b635 100644 --- a/dataAnalysis/VariantCalling/gatk-dnaseq-best-practices-workflow.md +++ b/dataAnalysis/VariantCalling/gatk-dnaseq-best-practices-workflow.md @@ -12,10 +12,6 @@ header: # GATK Best Practices Workflow for DNA-Seq -## Introduction - -Link Andrew's GATK introduction here or borrow his text. - ## Dataset For this tutorial we will use the dataset from BioProject [PRJEB18647](https://www.ncbi.nlm.nih.gov/bioproject/PRJEB18647). This dataset has Illumina short reads for four different populations of _Arabidopsis halleri_ subsp. _halleri_ (Aha18, AhaN1, AhaN3, AhaN4) and was originally used for estimating genomic diversity and population differentiation for these 4 populations ([Fischer _et. al_.,](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3459-7)). From 51a6e3259e6ebe70dfaf6b65c63554028ed680c0 Mon Sep 17 00:00:00 2001 From: Ephantus Wambui <58903181+Ephantus-Wambui@users.noreply.github.com> Date: Wed, 25 Oct 2023 21:28:01 +0300 Subject: [PATCH 2/3] fix typo (#68) --- Appendix/Unix/unix-basics-1.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Appendix/Unix/unix-basics-1.md b/Appendix/Unix/unix-basics-1.md index 5bfd921c..56b9faad 100644 --- a/Appendix/Unix/unix-basics-1.md +++ b/Appendix/Unix/unix-basics-1.md @@ -453,7 +453,7 @@ ls Deleteme3 ### Warning about deleting files and directories -In Unix there is no undo command. If you delete a file it is gone. There is no trash bin. The next two commands are very powerful commands and cna lead to unfortunate losses if not used with care. With that said you can only delete files you have created. So it is impossible to delete someone else files without permission. +In Unix there is no undo command. If you delete a file it is gone. There is no trash bin. The next two commands are very powerful commands and can lead to unfortunate losses if not used with care. With that said you can only delete files you have created. So it is impossible to delete someone else files without permission. ## `rmdir` -- Remove Directory This command can remove an empty directory From dc0d700a451cdf554f4ff1dd72f17f0a102f153b Mon Sep 17 00:00:00 2001 From: Christopher Bottoms Date: Wed, 25 Oct 2023 14:52:53 -0500 Subject: [PATCH 3/3] Update UnixCheatSheet.md (#59) Removed extraneous words "found at found here" -> "found here" Updated command formatting and added "previous directory" command `cd -` --- Appendix/Unix/UnixCheatSheet.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/Appendix/Unix/UnixCheatSheet.md b/Appendix/Unix/UnixCheatSheet.md index 6a245a7f..a2e781ef 100644 --- a/Appendix/Unix/UnixCheatSheet.md +++ b/Appendix/Unix/UnixCheatSheet.md @@ -16,8 +16,9 @@ header: | _Command_|_Function_|_Syntax/example usage_ | |`ls` |list contents |`ls` [OPTIONS] DIRECTORY| |`pwd` |print working directory |`pwd`| -|`cd`|change directory |`cd` ~ or `cd` #home directory| -| | |`cd` .. #previous (parent directory)| +|`cd`|change directory |`cd ~` or `cd` #home directory| +| | |`cd ..` #"up" a directory (parent directory)| +| | |`cd -` # previous directory | ## File/Directory operations @@ -206,4 +207,4 @@ header: |||`module avail` # lists available modules| |||`module unload` PROGRAM # unloads module| -PS: An A-Z Index of the Bash command line for Linux can be found at found [Here](http://ss64.com/bash/index.html) +PS: An A-Z Index of the Bash command line for Linux can be found [here](http://ss64.com/bash/index.html)