From 0d2b4814ac5ba244bb5ac45e72d34de76646ef2d Mon Sep 17 00:00:00 2001
From: Endre Bakken Stovner <endrebak85@gmail.com>
Date: Thu, 5 Dec 2019 13:45:05 +0100
Subject: [PATCH 1/2] Allow prefix in config file

This allows users to run different analyses from the folder
in which the Snakefile is located.
---
 Snakefile           | 19 ++++++++++---------
 config_example.yaml |  3 +++
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/Snakefile b/Snakefile
index 323b83e..3a12330 100644
--- a/Snakefile
+++ b/Snakefile
@@ -19,19 +19,20 @@ def get_region(wildcards):
 
 rule all:
     input:
-        expand("methylation_frequency/{region}_{sample}.tsv",
+        expand("{prefix}methylation_frequency/{region}_{sample}.tsv",
                sample=config["fastq"],
-               region=config["region"])
+               region=config["region"],
+               prefix=config.get("prefix", ""))
 
 rule nanopolish_index:
     input:
         f5 = get_fast5,
         fq = get_fastq,
     output:
-        "indices/index_done_{sample}"
+        "{prefix}indices/index_done_{sample}"
     threads: 10  # Just to ensure that this is not ran in parallel for too many samples
     log:
-        "logs/nanopolish_index/index_{sample}.log"
+        "{prefix}logs/nanopolish_index/index_{sample}.log"
     shell:
         """
         nanopolish index -d {input.f5}/ {input.fq} 2> {log}
@@ -45,12 +46,12 @@ rule call_methylation:
         bam = get_bam,
         genome = config["genome"],
     output:
-        "methylation_calls/{region}_{sample}.tsv"
+        "{prefix}methylation_calls/{region}_{sample}.tsv"
     threads: 8
     params:
         region = get_region,
     log:
-        "logs/methylation/methcall_{region}_{sample}.log"
+        "{prefix}logs/methylation/methcall_{region}_{sample}.log"
     shell:
         """
         nanopolish call-methylation \
@@ -63,11 +64,11 @@ rule call_methylation:
 
 rule methylation_frequency:
     input:
-        "methylation_calls/{region}_{sample}.tsv"
+        "{prefix}methylation_calls/{region}_{sample}.tsv"
     output:
-        "methylation_frequency/{region}_{sample}.tsv"
+        "{prefix}methylation_frequency/{region}_{sample}.tsv"
     log:
-        "logs/methylation/methfreq_{region}_{sample}.log"
+        "{prefix}logs/methylation/methfreq_{region}_{sample}.log"
     params:
         script = os.path.join(workflow.basedir, "scripts/calculate_methylation_frequency.py")
     shell:
diff --git a/config_example.yaml b/config_example.yaml
index b63421f..d5148f3 100644
--- a/config_example.yaml
+++ b/config_example.yaml
@@ -1,3 +1,6 @@
+prefix:
+  "analysis_name"
+
 genome:
     /path/to/database/genome.fa.gz
 

From b36164dd0366d4a9b1985ceb16a26383e2c73489 Mon Sep 17 00:00:00 2001
From: Endre Bakken Stovner <endrebak85@gmail.com>
Date: Thu, 5 Dec 2019 13:50:50 +0100
Subject: [PATCH 2/2] Update config with example prefix

---
 config_example.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config_example.yaml b/config_example.yaml
index d5148f3..696cc4b 100644
--- a/config_example.yaml
+++ b/config_example.yaml
@@ -1,5 +1,5 @@
 prefix:
-  "analysis_name"
+  "analysis_name" # or /path/where/you/want/the/results
 
 genome:
     /path/to/database/genome.fa.gz