From d789a13be15cd8ebb3621946fafbf558b15f0658 Mon Sep 17 00:00:00 2001
From: msbentsen <mette.bentsen@mpi-bn.mpg.de>
Date: Mon, 6 Jan 2020 10:17:44 +0100
Subject: [PATCH] Added exception for configfiles depending on snakemake
 version

---
 Snakefile                      |  7 ++++-
 environments/tobias.yaml       | 56 +++++++++-------------------------
 snakefiles/preprocessing.snake |  8 +++--
 3 files changed, 26 insertions(+), 45 deletions(-)

diff --git a/Snakefile b/Snakefile
index d85f306..0147099 100644
--- a/Snakefile
+++ b/Snakefile
@@ -8,11 +8,16 @@ import itertools
 import glob
 import datetime
 
+snakemake.utils.min_version("5.4")	#for checkpoints functionality
+
 #-------------------------------------------------------------------------------#
 #---------------------- SETUP PROCESS-RELATED CONFIGURATION --------------------#
 #-------------------------------------------------------------------------------#
+try:
+	CONFIGFILE = str(workflow.overwrite_configfiles[0])
+except:
+	CONFIGFILE = str(workflow.overwrite_configfile[0])
 
-CONFIGFILE = str(workflow.overwrite_configfile)
 wd = os.getcwd()
 config["wd"] = wd
 
diff --git a/environments/tobias.yaml b/environments/tobias.yaml
index fac19df..15c7494 100644
--- a/environments/tobias.yaml
+++ b/environments/tobias.yaml
@@ -5,49 +5,23 @@ channels:
   - conda-forge
 
 dependencies:
-  - python >= 3
-  - pysam
-  - pybigwig
+  - python=3
+  - snakemake>=5.4
+  - uropa=3
+  - samtools
   - moods
-  - pybedtools
-  - cython
-  - matplotlib
-  - numpy
-  - scipy
-  - pypdf2
-  - scikit-learn
-  - snakemake
-  - bedtools
-  - uropa
-  - igvtools
-  - openjdk
-  - xlsxwriter
-  - cloudpickle = 0.5.6
   - unzip
-  - r-base
   - r-devtools
-  - r-shiny
-  - r-data.table
-  - r-ggplot2
-  - r-plotly
+  - r-knitr
+  - r-lme4
+  - r-htmltable
+  - tobias>=0.9
+  - r-hmisc
+  - r-pbkrtest
+  - r-openxlsx
+  - r-rio
+  - r-car
   - bioconductor-deseq2
-  - r-plyr
-  - r-scales
-  - r-rjson
-  - r-shinydashboard
-  - r-reshape
-  - r-ggrepel >= 0.6.12
-  - r-heatmaply >= 0.14.1
-  - r-colorspace
-  - r-shinyjs
-  - r-viridis
-  - r-rje
-  - r-openssl
-  - r-shinycssloaders
-  - r-log4r
-  - r-shinythemes
-  - r-shinybs
   - intervene
-  - pip: 
-    - adjustText
-    - tobias
+  - igvtools
+  - icu
diff --git a/snakefiles/preprocessing.snake b/snakefiles/preprocessing.snake
index d8df927..8284c02 100644
--- a/snakefiles/preprocessing.snake
+++ b/snakefiles/preprocessing.snake
@@ -94,7 +94,7 @@ rule process_peaks:
 		peaks = lambda wildcards: [os.path.join(OUTPUTDIR, "peak_calling", wildcards.condition, sample_id + "_raw.bed") for sample_id in id2bam[wildcards.condition].keys()],
 		blacklisted = BLACKLIST
 	output: 
-		peaks = os.path.join(OUTPUTDIR, "peak_calling", "{condition}_union.bed"),
+		peaks = os.path.join(OUTPUTDIR, "peak_calling", "{condition}_union.bed")
 	message: "Processing peaks from condition {wildcards.condition}"
 	shell:
 		"cat {input.peaks} | cut -f1-3 | sort -k1,1 -k2,2n | bedtools merge -d 5 | bedtools subtract -a - -b {input.blacklisted} -A | "
@@ -103,8 +103,10 @@ rule process_peaks:
 
 # Union peaks across all conditions
 rule merge_condition_peaks:
-	input: expand(rules.process_peaks.output.peaks, condition=CONDITION_IDS)  #expand(os.path.join(OUTPUTDIR, "peak_calling", "{condition}_union.bed"), condition=CONDITION_IDS)
-	output: temp(os.path.join(OUTPUTDIR, "peak_calling", "all_merged.tmp"))
+	input: 
+		[os.path.join(OUTPUTDIR, "peak_calling", condition + "_union.bed") for condition in CONDITION_IDS]
+	output: 
+		temp(os.path.join(OUTPUTDIR, "peak_calling", "all_merged.tmp"))
 	message: "Merging peaks across conditions"
 	shell:
 		"cat {input} | sort -k1,1 -k2,2n | bedtools merge -d 5 -c 4 -o distinct > {output}"