From f81488ec89666a866eedba604482b77a0bb03f83 Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Tue, 7 Mar 2017 10:22:38 -0600
Subject: [PATCH] Fixed issues with ccat output files.
---
chipathlon/jobs/modules/peak_call.yaml | 17 +++++++++++------
chipathlon/peak_call_generator.py | 2 +-
2 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/chipathlon/jobs/modules/peak_call.yaml b/chipathlon/jobs/modules/peak_call.yaml
index 97d2bd2..31b68f6 100644
--- a/chipathlon/jobs/modules/peak_call.yaml
+++ b/chipathlon/jobs/modules/peak_call.yaml
@@ -49,25 +49,30 @@ peak_call:
type: string
additional_inputs: null
outputs:
- - ccat.significant.peak:
+ - significant.peak:
type: file
- - ccat.significant.region:
+ prefix_join: "."
+ - significant.region:
type: file
- - ccat.top100000.peak:
+ prefix_join: "."
+ - top100000.peak:
type: file
- - ccat.log:
+ prefix_join: "."
+ - log:
type: stdout
+ prefix_join: "."
- ccat_format_bed:
inputs:
- - ccat.significant.region:
+ - significant.region:
type: file
additional_inputs: null
outputs:
- region_sorted.bed:
type: file
+ save_result: true
- ccat_format_bed:
inputs:
- - ccat.significant.peak:
+ - significant.peak:
type: file
additional_inputs: null
outputs:
diff --git a/chipathlon/peak_call_generator.py b/chipathlon/peak_call_generator.py
index a305229..6b6b0d7 100644
--- a/chipathlon/peak_call_generator.py
+++ b/chipathlon/peak_call_generator.py
@@ -70,7 +70,7 @@ class PeakCallGenerator(ModuleGenerator):
# The prefix mod is because ccat files have double extensions,
# and we can't control the names of the output files directly,
# only with the prefix.
- "prefix": "_".join(result.prefix.split("_")[:-1])
+ "prefix": result.prefix
}
additional_inputs = {}
return (markers, inputs, additional_inputs)
--
GitLab