Commit 1994ee66 authored by aknecht2's avatar aknecht2
Browse files

Updates to make sure jobs get loaded correctly with executable changes.

parent 59287112
......@@ -45,8 +45,15 @@ executables = [
"bamtools",
"samtools",
"idr",
"picard"
] + align_tools + peak_tools
"picard",
"bwa",
"bowtie2",
"macs2",
"gem",
"peakranger",
"MUSIC",
"CCAT"
]
# Peak_type validation
peak_types = {
......
......@@ -35,7 +35,7 @@ ccat_callpeak:
- name: ccat_log
type: stdout
file_type: log
command: ccat
command: CCAT
arguments:
- "$inputs.0":
type: file
......
......@@ -42,7 +42,7 @@ music_broad:
- name: scale_16626.bed
type: file
file_type: bed
command: music
command: MUSIC
arguments:
- "--prefix":
type: string
......
......@@ -26,7 +26,7 @@ music_narrow:
- name: scale_291.bed
type: file
file_type: bed
command: music
command: MUSIC
arguments:
- "--prefix":
type: string
......
......@@ -46,7 +46,7 @@ music_punctate:
- name: scale_2216.bed
type: file
file_type: bed
command: music
command: MUSIC
arguments:
- "--prefix":
type: string
......
......@@ -20,7 +20,7 @@ spp_nodups_broad:
- name: score
type: file
file_type: ccscore
command: spp_nodups
command: run_spp_nodups
arguments:
- "-c=":
type: file
......
......@@ -20,7 +20,7 @@ spp_nodups_narrow:
- name: score
type: file
file_type: ccscore
command: spp_nodups
command: run_spp_nodups
arguments:
- "-c=":
type: file
......
......@@ -481,6 +481,8 @@ class WorkflowJob(object):
"$outputs": outputs
}
arg_list = []
if self.executable == "gem":
arg_list.append("-Xmx%sM" % (self.params.get("memory", self.job_data["memory"])))
has_args = re.compile("\$((in)|(out))puts\.[0-9]")
# Loop through each argument, which are stored as a list of dicts
for arg_dict in self.job_data["arguments"]:
......
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