Commit 738e3744 authored by aknecht2's avatar aknecht2
Browse files

Fixed peak calling workflow generation, updated configuration and yaml files.

parent acdc8601
......@@ -21,7 +21,9 @@ file_extensions = {
"bwa_genome": ["amb", "ann", "bwt", "pac", "sa"],
"bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"],
"quality": ["quality"],
"qc": ["qc"]
"qc": ["qc"],
"pdf": ["pdf"],
"ccscore": ["ccscore"]
}
# list of resources that can be specified per job (step) in
......
......@@ -6,6 +6,7 @@ macs2_callpeak:
type: file
- prefix:
type: argument
additional_inputs: null
outputs:
- bed:
type: file
......
......@@ -4,6 +4,7 @@ r_spp_nodups:
type: file
- bam:
type: file
additional_inputs: null
outputs:
- bed:
type: file
......@@ -42,17 +43,17 @@ r_spp_nodups:
changeable: false
required: true
has_value: true
default: $outputs.1
default: $outputs.0
- "-savp":
changeable: false
required: true
has_value: true
default: $outputs.2
default: $outputs.1
- "-out":
changeable: false
required: true
has_value: true
default: $outputs.3
default: $outputs.2
- "-fdr":
changeable: true
required: false
......
......@@ -2,6 +2,7 @@ sort_awk_sort_peaks:
inputs:
- bed:
type: file
additional_inputs: null
outputs:
- bed:
type: file
......
......@@ -2,6 +2,7 @@ zcat_awk_sort_peaks:
inputs:
- bed:
type: file
additional_inputs: null
outputs:
- bed:
type: file
......
......@@ -58,6 +58,7 @@ class Workflow(object):
self._add_download()
self._add_align()
self._add_remove_duplicates()
self._add_peak_calling()
# Create pegasus important stuff
self._create_setup()
self._add_notify()
......@@ -334,11 +335,9 @@ class Workflow(object):
# prefix and add in as input_files
# remove_duplicates returns prefix_no_dups.bam
# REMEMBER: experiment is always first
final_prefix = ""
for i, file_tuple in enumerate(pair):
prefix = run["prefix"][i]
inputs["exp.bam"] = prefix + "_no_dups.bam"
final_prefix += prefix
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"
if run["peak"] == "spp":
pass
elif run["peak"] == "macs2":
......
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