From ac3a4e0363c1fde0f1dbff75b95aa27d9acd5e5e Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 10 Oct 2022 13:22:03 +1100 Subject: insert exercise 4 --- day2/ex4-bwa/default.nix | 52 ------------------------------------------------ 1 file changed, 52 deletions(-) delete mode 100644 day2/ex4-bwa/default.nix (limited to 'day2/ex4-bwa/default.nix') diff --git a/day2/ex4-bwa/default.nix b/day2/ex4-bwa/default.nix deleted file mode 100644 index 9c8356a..0000000 --- a/day2/ex4-bwa/default.nix +++ /dev/null @@ -1,52 +0,0 @@ -/* -BioNix is a thin wrapper over Nix: there is not much functionality -required for pipelining that is not already present in the base build -engine. As such, the focus is on providing an interface that is -convenient for specifying common bioinformatics workflows. To this end, -BioNix provides a library of tools to help simplify the specification of -common bioinformatics pipelines, with a notable focus on genomics tools. -You can see the available tools at -https://github.com/PapenfussLab/bionix/tree/master/tools. - -This exercise aims to demonstrate how to both use a tool available in -BioNix on some input data and how to chain them together. We will do a -simple alignment with BWA on some simulated reads from a bacterial -genome. The BWA tool is provided by -https://github.com/PapenfussLab/bionix/blob/master/tools/bwa.nix and as -you can see there are alignment functions for alignment with BWA/BWA2, -as well as corresponding index functions for indexing a reference -genome. Don't worry about indexing, this will be handled automatically, -you only have to declare you want an alignment and what genome and the -index will be generated if needed. - -Exercise: - -1. Sample data along with a reference will be fetched from github. As -before, hashes of the content must be known. Fill in the hashes to fully -specify the inputs. - -2. With the hashes in place, the expression should evaluate and BWA -should run. Try swapping BWA out with some of the other available -aligners in BioNix (e.g., bowtie, hisat2, minimap2, whisper). - -3. Aligners produce *unsorted* output, but co-ordinate sorted alignments -are usually desired as they are indexable by position. Pass the aligned -output to the samtools sort function to sort the alignments into co- -ordinate order. -*/ -{bionix}: -with bionix; let - input = { - input1 = fetchFastQ { - url = "https://raw.githubusercontent.com/PapenfussLab/bionix/bac9248a5e08e8afdf5485a6e27cfe72e1ca5090/examples/sample1-1.fq"; - }; - input2 = fetchFastQ { - url = "https://raw.githubusercontent.com/PapenfussLab/bionix/bac9248a5e08e8afdf5485a6e27cfe72e1ca5090/examples/sample1-2.fq"; - }; - }; - - ref = fetchFastA { - url = "https://raw.githubusercontent.com/PapenfussLab/bionix/bac9248a5e08e8afdf5485a6e27cfe72e1ca5090/examples/ref.fa"; - }; -in - bwa.align {} input -- cgit v1.2.3