Commit 932ac021 authored by aknecht2's avatar aknecht2
Browse files

Gem ONLY accepts chr_fasta files with names chr1.fa, chr2.fa... We can't...

Gem ONLY accepts chr_fasta files with names chr1.fa, chr2.fa... We can't prefix them with our unique genome prefix, so we are now staging them into separate directories based on assembly.
parent 887a3012
......@@ -125,6 +125,6 @@ class Genome(object):
for root, dirs, files in os.walk(base_dir):
for f in files:
if f.startswith("chr"):
self._add_file("%s_%s" % (self.add_file_prefix, f), root + "/" + f, "chr_fasta")
self._add_file("%s/%s" % (self.assembly, os.path.basename(f)), os.path.join(root, f), "chr_fasta")
break
return
......@@ -76,6 +76,8 @@ peak_call:
type: file
- prefix:
type: string
- genome_dir:
type: string
additional_inputs:
- read.dist:
type: file
......
......@@ -14,6 +14,9 @@ gem_callpeak:
- name: prefix
type: string
- name: genome
type: string
additional_inputs:
- name: read_distribution
type: file
......@@ -54,18 +57,18 @@ gem_callpeak:
required: true
has_value: true
default: $inputs.2
- "--genome":
type: string
changeable: false
required: true
has_value: true
default: "."
- "--out":
type: argument
changeable: false
required: true
has_value: true
default: $inputs.3
- "--genome":
type: string
changeable: false
required: true
has_value: true
default: "$inputs.4"
- "--k_min":
type: numeric
changeable: true
......
......@@ -85,7 +85,8 @@ class PeakCallGenerator(ModuleGenerator):
"chrom.sizes": run.genome.get_chrom_sizes()["name"],
"control.bed": call_pair[0].full_name,
"exp.bed": call_pair[1].full_name,
"prefix": result.prefix
"prefix": result.prefix,
"genome_dir": run.genome.assembly
}
additional_inputs = {
"read.dist": self.module.workflow_jobs["gem_callpeak"].raw_files.keys()[0],
......
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