fix: harmonize config.yaml files (incl. .test/config/)

.test/config/config.yaml

@@ -15,4 +15,32 @@ ref:
   # Optionally, instead of downloading the whole reference from Ensembl via the 
   # parameters above, specify a specific chromosome below and uncomment the line.
   # This is usually only relevant for testing.
-  chromosome: 7
+  chromosome: 7
+
+# These filters mostly correspond to the output columns of Circle-Map:
+# https://github.com/iprada/Circle-Map/wiki/Circle-Map-Realign-output-files
+# In addition, you can filter on the length of the circle.
+circle_filtering:
+  min_circle_score: 100
+  min_split_reads: 0
+  min_discordant_read_pairs: 0
+  max_uncovered_fraction: 0.8
+  min_mean_coverage: 2.5
+  min_circle_length: 500
+  max_circle_length: 80000000
+
+# You can pass extra command line arguments to the following tools. However, it is
+# very unlikely that you will need this functionality. Usually, all tools should be
+# configured correctly for the purposes of this analysis out of the box.
+# 
+# Also note, that this section is NOT for specifying resources that a rule might
+# want to reserve. Please directly annotate the rules via the `resources:` directive
+# if you have to specify those (for example for a cluster / scheduler that needs them).
+# For details on resource specifications, see:
+# https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources
+params:
+  cutadapt: ""
+  gatk:
+    BaseRecalibrator: ""
+    applyBQSR: ""
+

config/config.yaml

@@ -17,6 +17,18 @@ ref:
   # This is usually only relevant for testing.
   # chromosome: 21
 
+# These filters mostly correspond to the output columns of Circle-Map:
+# https://github.com/iprada/Circle-Map/wiki/Circle-Map-Realign-output-files
+# In addition, you can filter on the length of the circle.
+circle_filtering:
+  min_circle_score: 100
+  min_split_reads: 0
+  min_discordant_read_pairs: 0
+  max_uncovered_fraction: 0.8
+  min_mean_coverage: 2.5
+  min_circle_length: 500
+  max_circle_length: 80000000
+
 # You can pass extra command line arguments to the following tools. However, it is
 # very unlikely that you will need this functionality. Usually, all tools should be
 # configured correctly for the purposes of this analysis out of the box.
@@ -32,14 +44,3 @@ params:
     BaseRecalibrator: ""
     applyBQSR: ""
 
-# These filters mostly correspond to the output columns of Circle-Map:
-# https://github.com/iprada/Circle-Map/wiki/Circle-Map-Realign-output-files
-# In addition, you can filter on the length of the circle.
-circle_filtering:
-  min_circle_score: 100
-  min_split_reads: 1
-  min_discordant_read_pairs: 1
-  max_uncovered_fraction: 0.9
-  min_mean_coverage: 2.0
-  min_circle_length: 500
-  max_circle_length: 80000000