Commit 4a164e8b authored by aknecht2's avatar aknecht2
Browse files

Added bedtools bamtobed.

parent 277de0d8
......@@ -2,9 +2,9 @@ peak_call:
- spp[tool]:
- r_spp_nodups:
inputs:
- exp.bam:
- exp.bed:
type: file
- control.bam:
- control.bed:
type: file
additional_inputs: null
outputs:
......@@ -25,9 +25,9 @@ peak_call:
- macs2[tool]:
- macs2_callpeak:
inputs:
- exp.bam:
- exp.bed:
type: file
- control.bam:
- control.bed:
type: file
- prefix:
type: argument
......
......@@ -25,3 +25,11 @@ remove_duplicates:
type: file
- quality.qc:
type: file
- bedtools_bam_to_bed:
inputs:
- no_dups.bam:
type: file
additional_inputs: null
outputs:
- no_dups.bed:
type: file
......@@ -291,7 +291,7 @@ class Workflow(object):
job.addArguments("-u", f["url"], "-p", output_file, "-t http://", "-m", f["md5sum"])
self.jobs[name] = job
self.dax.addJob(job)
# USING PEGASUS TRANSFER:
# USING PEGASUS TRANSFER:
# self._add_file(name, "http://" + f["url"], "dummylocal")
# We additionally keep track of how many input files
# there are to increase the number of transfer
......@@ -359,8 +359,8 @@ class Workflow(object):
# remove_duplicates returns prefix_no_dups.bam
# REMEMBER: experiment is always first
final_prefix = run["prefix"][0] + "_" + run["prefix"][1]
inputs["exp.bam"] = run["prefix"][0] + "_no_dups.bam"
inputs["control.bam"] = run["prefix"][1] + "_no_dups.bam"
inputs["exp.bed"] = run["prefix"][0] + "_no_dups.bed"
inputs["control.bed"] = run["prefix"][1] + "_no_dups.bed"
if run["peak"] == "spp":
pass
elif run["peak"] == "macs2":
......
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