Merge pull request #245 from karel-brinda/download_asms

Add `make download_asms` and `make download_cobs`

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")
@@ -71,6 +71,12 @@ conda: ## Create the conda environments
 download: ## Download the assemblies and COBS indexes
 	snakemake download $(SMK_PARAMS) -j 99999
 
+download_asms: ## Download only the assemblies
+	snakemake download_asms_batches $(SMK_PARAMS) -j 99999
+
+download_cobs: ## Download only 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)"
 

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)
 ###############

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.
     """