Commit 1e99f93c authored by Tizian Schulz's avatar Tizian Schulz
Browse files

Unparallelized data download

parent c8bedd35
......@@ -147,6 +147,8 @@ rule createReadList:
rule downloadReadSets:
input:
"arabidopsis/reads/filereport_read_run_PRJEB2457_tsv.txt"
threads:
workflow.cores
output:
["arabidopsis/reads/" + basename(f) for l in open("arabidopsis/reads/filereport_read_run_PRJEB2457_tsv.txt", 'r') for f in l.split('\t')[6].split(';')]
shell:
......@@ -165,6 +167,8 @@ rule createAssemblyList:
rule getNCBI_Genomes:
input:
"{sp}/genomeSequences/accessions.txt"
threads:
workflow.cores
output:
"{sp}/genomeSequences/{acc}.fasta"
shell:
......@@ -173,6 +177,8 @@ rule getNCBI_Genomes:
rule getArabidopsisGenomes:
input:
"arabidopsis/genomeSequences/links.txt"
threads:
workflow.cores
output:
expand("arabidopsis/genomeSequences/{g}", g=[basename(u.strip()) for u in open("arabidopsis/genomeSequences/links.txt", 'r')])
shell:
......
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