From ba382ab81c626e80487edc503e7d88917a05204c Mon Sep 17 00:00:00 2001 From: Francii-B Date: Wed, 29 Nov 2023 16:41:55 +0100 Subject: [PATCH 1/3] Added subcommands download_asms and download_cobs --- Makefile | 6 ++++++ Snakefile | 13 +++++++++++++ 2 files changed, 19 insertions(+) diff --git a/Makefile b/Makefile index 29e569b..3421e31 100644 --- a/Makefile +++ b/Makefile @@ -71,6 +71,12 @@ conda: ## Create the conda environments download: ## Download the assemblies and COBS indexes snakemake download $(SMK_PARAMS) -j 99999 +download_asms: ## Download the assemblies + snakemake download_asms_batches $(SMK_PARAMS) -j 99999 + +download_cobs: ## Download the COBS indexes + snakemake download_cobs_batches $(SMK_PARAMS) -j 99999 + match: ## Match queries using COBS (queries -> candidates) scripts/benchmark.py --log logs/benchmarks/match_$(DATETIME).txt "snakemake match $(SMK_PARAMS)" diff --git a/Snakefile b/Snakefile index 871eeba..6a52aef 100644 --- a/Snakefile +++ b/Snakefile @@ -225,6 +225,19 @@ rule download: [f"{cobs_dir}/{x}.cobs_classic.xz" for x in batches], +rule download_asms_batches: + """Download assemblies. + """ + input: + [f"{assemblies_dir}/{x}.tar.xz" for x in batches], + + +rule download_cobs_batches: + """Download COBS indexes. + """ + input: + [f"{cobs_dir}/{x}.cobs_classic.xz" for x in batches], + rule match: """Match reads to the COBS indexes. """ From ab54a05a078d3e3ffcb75d9b89a69c1360591b53 Mon Sep 17 00:00:00 2001 From: Francii-B Date: Wed, 29 Nov 2023 17:08:55 +0100 Subject: [PATCH 2/3] Update phony rules --- Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index 3421e31..deaa458 100644 --- a/Makefile +++ b/Makefile @@ -1,4 +1,4 @@ -.PHONY: all test help clean cleanall cluster download match map format report viewconf conda +.PHONY: all test help clean cleanall cluster download download_asms download_cobs match map format report viewconf conda SHELL=/usr/bin/env bash -eo pipefail DATETIME=$(shell date -u +"%Y_%m_%dT%H_%M_%S") @@ -71,10 +71,10 @@ conda: ## Create the conda environments download: ## Download the assemblies and COBS indexes snakemake download $(SMK_PARAMS) -j 99999 -download_asms: ## Download the assemblies +download_asms: ## Download only the assemblies snakemake download_asms_batches $(SMK_PARAMS) -j 99999 -download_cobs: ## Download the COBS indexes +download_cobs: ## Download only the COBS indexes snakemake download_cobs_batches $(SMK_PARAMS) -j 99999 match: ## Match queries using COBS (queries -> candidates) From 61ad22bcc157ccee4270d9613a17582481d1e1f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Wed, 29 Nov 2023 17:14:35 +0100 Subject: [PATCH 3/3] Update make subcommands in the readme --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 0c8fee9..dabdf5e 100644 --- a/README.md +++ b/README.md @@ -246,6 +246,8 @@ Here's a list of all implemented commands (to be executed as `make {command}`): #################### conda Create the conda environments download Download the assemblies and COBS indexes + download_asms Download only the assemblies + download_cobs Download only the COBS indexes match Match queries using COBS (queries -> candidates) map Map candidates to assemblies (candidates -> alignments) ###############