Commit 7a42ce0b authored by Tizian Schulz's avatar Tizian Schulz
Browse files

Merge branch 'dev' into 'master'

Removed download rules from workflow

See merge request !2
parents ebcd3fcb fda312b4
......@@ -144,15 +144,15 @@ rule createReadList:
shell:
"ls -l {input} | tr -s ' ' | cut -d' ' -f9 > {output}"
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:
"wget $(python3 scripts/getReadLocations.py {input}); mv *.fastq.gz arabidopsis/reads"
# 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(';') if f != "fastq_ftp"]
# shell:
# "wget $(python3 scripts/getReadLocations.py {input}); mv *.fastq.gz arabidopsis/reads"
rule createAssemblyList:
input:
......@@ -164,25 +164,25 @@ rule createAssemblyList:
shell:
"ls -l {input} | tr -s ' ' | cut -d' ' -f9 > {output}"
rule getNCBI_Genomes:
input:
"{sp}/genomeSequences/accessions.txt"
threads:
workflow.cores
output:
"{sp}/genomeSequences/{acc}.fasta"
shell:
"python3 scripts/get_fastas_for_acc_list.py {input}"
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:
"for u in $(cat {input}); do wget $u; done; mv *.fas arabidopsis/genomeSequences"
# rule getNCBI_Genomes:
# input:
# "{sp}/genomeSequences/accessions.txt"
# threads:
# workflow.cores
# output:
# "{sp}/genomeSequences/{acc}.fasta"
# shell:
# "python3 scripts/get_fastas_for_acc_list.py {input}"
# 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:
# "for u in $(cat {input}); do wget $u; done; mv *.fas arabidopsis/genomeSequences"
rule runPanaroo:
input:
......
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