From 890fe52a8ac98690ed68f30ee0a9ad79fcf84d19 Mon Sep 17 00:00:00 2001
From: Christian Arnold <christian.arnold@embl.de>
Date: Tue, 11 Jan 2022 15:07:48 +0100
Subject: [PATCH] Dev: Updated configuration files

---
 example/dev/input/config.yaml          | 7 +++----
 example/templates/dev/hg19/config.yaml | 9 ++++-----
 example/templates/dev/hg38/config.yaml | 7 +++----
 example/templates/dev/mm10/config.yaml | 7 +++----
 4 files changed, 13 insertions(+), 17 deletions(-)

diff --git a/example/dev/input/config.yaml b/example/dev/input/config.yaml
index 7f35028..caf721a 100644
--- a/example/dev/input/config.yaml
+++ b/example/dev/input/config.yaml
@@ -223,11 +223,10 @@ par_peakCalling:
 #########################
 par_deepTools:
 
-  # INTEGER. The default depends on the genome assembly, see the templates for details. Length of the “mappable” genome in bp as defined by deepTools (see https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html).
-  #effectiveGenomeSize: 2750000000
-  readLength: ""
+  # INTEGER. Read length. Default 100. Either 50, 100, 150, or 200. Based on this value, we provide automated estimates of the effective genome size as used in deepTools. If your read length is not one of them, approximate by rounding to the closest of the available options
+  readLength: 100
 
-  # STRING. Default “normalizeTo1x”. Either "normalizeTo1x NUMBER" OR "normalizeUsingRPKM" (note the missing (!) leading "--"), where NUMBER denotes the number of base pairs that are mappable. Beware of the mapping dependence on the read length for this number: The reported numbers on the websites are for 30bp reads, and we now have much longer reads usually. See Koehler et al. (2011) for numbers1.
+  # STRING. Default “RPGC”. Possible choices: RPKM, CPM, BPM, RPGC, None. See https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
   bamCoverage_normalizationCoverage: "RPGC"
 
   # INTEGER. Default 10. Size of the bins, in bases
diff --git a/example/templates/dev/hg19/config.yaml b/example/templates/dev/hg19/config.yaml
index 7324de0..5801dab 100644
--- a/example/templates/dev/hg19/config.yaml
+++ b/example/templates/dev/hg19/config.yaml
@@ -58,7 +58,7 @@ samples:
   # STRING. No default. Absolute path to the sample summary file. See section 2.4 for details.
   summaryFile: "/FULL/PATH/TO/samples.csv"
 
-  # BOOLEAN. “true” or “false”. Default “true”. Paired-end data? 
+  # BOOLEAN. “true” or “false”. Default “true”. Paired-end data?
   pairedEnd: true
 
   # STRING. "ATACseq" or "ChIPseq". Only data type specific steps are executed. Currently, if set to ChIP-Seq, ATAC-seq specific steps like RSS adjustment are not executed.
@@ -222,11 +222,10 @@ par_peakCalling:
 #########################
 par_deepTools:
 
-  # INTEGER. The default depends on the genome assembly, see the templates for details. Length of the “mappable” genome in bp as defined by deepTools (see https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html).
-  #effectiveGenomeSize: 2750000000
-  readLength: ""
+  # INTEGER. Read length. Default 100. Either 50, 100, 150, or 200. Based on this value, we provide automated estimates of the effective genome size as used in deepTools. If your read length is not one of them, approximate by rounding to the closest of the available options
+  readLength: "TODO"
 
-  # STRING. Default “normalizeTo1x”. Either "normalizeTo1x NUMBER" OR "normalizeUsingRPKM" (note the missing (!) leading "--"), where NUMBER denotes the number of base pairs that are mappable. Beware of the mapping dependence on the read length for this number: The reported numbers on the websites are for 30bp reads, and we now have much longer reads usually. See Koehler et al. (2011) for numbers1.
+  # STRING. Default “RPGC”. Possible choices: RPKM, CPM, BPM, RPGC, None. See https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
   bamCoverage_normalizationCoverage: "RPGC"
 
   # INTEGER. Default 10. Size of the bins, in bases
diff --git a/example/templates/dev/hg38/config.yaml b/example/templates/dev/hg38/config.yaml
index ce27595..f277b0e 100644
--- a/example/templates/dev/hg38/config.yaml
+++ b/example/templates/dev/hg38/config.yaml
@@ -223,11 +223,10 @@ par_peakCalling:
 #########################
 par_deepTools:
 
-  # INTEGER. The default depends on the genome assembly, see the templates for details. Length of the “mappable” genome in bp as defined by deepTools (see https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html).
-  #effectiveGenomeSize: 2750000000
-  readLength: ""
+  # INTEGER. Read length. Default 100. Either 50, 100, 150, or 200. Based on this value, we provide automated estimates of the effective genome size as used in deepTools. If your read length is not one of them, approximate by rounding to the closest of the available options
+  readLength: "TODO"
 
-  # STRING. Default “normalizeTo1x”. Either "normalizeTo1x NUMBER" OR "normalizeUsingRPKM" (note the missing (!) leading "--"), where NUMBER denotes the number of base pairs that are mappable. Beware of the mapping dependence on the read length for this number: The reported numbers on the websites are for 30bp reads, and we now have much longer reads usually. See Koehler et al. (2011) for numbers1.
+  # STRING. Default “RPGC”. Possible choices: RPKM, CPM, BPM, RPGC, None. See https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
   bamCoverage_normalizationCoverage: "RPGC"
 
   # INTEGER. Default 10. Size of the bins, in bases
diff --git a/example/templates/dev/mm10/config.yaml b/example/templates/dev/mm10/config.yaml
index bed2412..8f8df34 100644
--- a/example/templates/dev/mm10/config.yaml
+++ b/example/templates/dev/mm10/config.yaml
@@ -221,11 +221,10 @@
   #########################
   par_deepTools:
 
-    # INTEGER. The default depends on the genome assembly, see the templates for details. Length of the “mappable” genome in bp as defined by deepTools (see https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html).
-    #effectiveGenomeSize: 2750000000
-    readLength: ""
+    # INTEGER. Read length. Default 100. Either 50, 100, 150, or 200. Based on this value, we provide automated estimates of the effective genome size as used in deepTools. If your read length is not one of them, approximate by rounding to the closest of the available options
+    readLength: "TODO"
 
-    # STRING. Default “normalizeTo1x”. Either "normalizeTo1x NUMBER" OR "normalizeUsingRPKM" (note the missing (!) leading "--"), where NUMBER denotes the number of base pairs that are mappable. Beware of the mapping dependence on the read length for this number: The reported numbers on the websites are for 30bp reads, and we now have much longer reads usually. See Koehler et al. (2011) for numbers1.
+    # STRING. Default “RPGC”. Possible choices: RPKM, CPM, BPM, RPGC, None. See https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
     bamCoverage_normalizationCoverage: "RPGC"
 
     # INTEGER. Default 10. Size of the bins, in bases
-- 
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