From c6f5a214353dcf6250880b7e99a3329b825c2dcb Mon Sep 17 00:00:00 2001
From: Jin wook Lee <leepc12@gmail.com>
Date: Thu, 24 Feb 2022 11:20:21 -0800
Subject: [PATCH 1/3] bump ver

---
 chip.wdl | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/chip.wdl b/chip.wdl
index 90ddfe9..66a383a 100644
--- a/chip.wdl
+++ b/chip.wdl
@@ -7,10 +7,10 @@ struct RuntimeEnvironment {
 }
 
 workflow chip {
-    String pipeline_ver = 'v2.1.4'
+    String pipeline_ver = 'v2.1.5'
 
     meta {
-        version: 'v2.1.4'
+        version: 'v2.1.5'
 
         author: 'Jin wook Lee'
         email: 'leepc12@gmail.com'
@@ -19,8 +19,8 @@ workflow chip {
 
         specification_document: 'https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit?usp=sharing'
 
-        default_docker: 'encodedcc/chip-seq-pipeline:v2.1.4'
-        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.sif'
+        default_docker: 'encodedcc/chip-seq-pipeline:v2.1.5'
+        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.5.sif'
         croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/chip.croo.v5.json'
 
         parameter_group: {
@@ -71,8 +71,8 @@ workflow chip {
     }
     input {
         # group: runtime_environment
-        String docker = 'encodedcc/chip-seq-pipeline:v2.1.4'
-        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.sif'
+        String docker = 'encodedcc/chip-seq-pipeline:v2.1.5'
+        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.5.sif'
         String conda = 'encode-chip-seq-pipeline'
         String conda_macs2 = 'encode-chip-seq-pipeline-macs2'
         String conda_spp = 'encode-chip-seq-pipeline-spp'

From 7a692c738d226bfc0f5f5ba283ab5ceba999248b Mon Sep 17 00:00:00 2001
From: Jin wook Lee <leepc12@gmail.com>
Date: Thu, 24 Feb 2022 14:12:19 -0800
Subject: [PATCH 2/3] fix conda ncurses issue

---
 scripts/install_conda_env.sh | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/scripts/install_conda_env.sh b/scripts/install_conda_env.sh
index 12d7b5c..4ee88fa 100755
--- a/scripts/install_conda_env.sh
+++ b/scripts/install_conda_env.sh
@@ -14,9 +14,12 @@ conda create -n encode-chip-seq-pipeline-macs2 --file ${SH_SCRIPT_DIR}/requireme
 conda create -n encode-chip-seq-pipeline-spp --file ${SH_SCRIPT_DIR}/requirements.spp.txt \
   --override-channels -c r -c bioconda -c defaults -y
 
-# adhoc fix for https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/259
-# force-install readline 6.2 from conda-forge (ignoring dependencies)
-conda install -n encode-chip-seq-pipeline-spp --no-deps --no-update-deps -y readline==6.2 -c conda-forge
+# adhoc fix for the following issues:
+# - https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/259
+# - https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/265
+# force-install readline 6.2, ncurses 5.9 from conda-forge (ignoring dependencies)
+conda install -n encode-chip-seq-pipeline-spp --no-deps --no-update-deps -y \
+  readline==6.2 ncurses==5.9 -c conda-forge
 
 echo "$(date): Done successfully."
 

From 93e91e7159dc057a4befb5df86fee534e78ff73a Mon Sep 17 00:00:00 2001
From: Jin wook Lee <leepc12@gmail.com>
Date: Mon, 28 Feb 2022 10:45:23 -0800
Subject: [PATCH 3/3] fix spp multithreading bug

---
 src/encode_task_spp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/encode_task_spp.py b/src/encode_task_spp.py
index 3d5b9a0..546d071 100755
--- a/src/encode_task_spp.py
+++ b/src/encode_task_spp.py
@@ -67,7 +67,7 @@ def spp(ta, ctl_ta, chrsz, fraglen, cap_num_peak, fdr_thresh,
     basename_prefix = '{}_x_{}'.format(basename_ta, basename_ctl_ta)
     if len(basename_prefix) > 200:  # UNIX cannot have filename > 255
         basename_prefix = '{}_x_control'.format(basename_ta)
-    nth_param = '-p={}'.format(nth) if nth < 2 else ''
+    nth_param = '-p={}'.format(nth) if nth >= 2 else ''
     prefix = os.path.join(out_dir, basename_prefix)
     rpeak = '{}.{}.regionPeak.gz'.format(
         prefix,