Maybe fix for cooltools wrappers? not tested

config/config.yaml → config/config.yml

@@ -1,32 +1,9 @@
 genome: hg38
-path_genome_folder: /exports/igmm/eddie/wendy-lab/ilia/genomes/hg38
-path_genome_fasta: /exports/igmm/eddie/wendy-lab/ilia/genomes/hg38/hg38.fa
-chromsizes: /exports/igmm/eddie/wendy-lab/ilia/genomes/hg38/chrfile.txt
-regions: /exports/igmm/eddie/wendy-lab/ilia/genomes/hg38/chrom_arms.txt
-ignore_chroms:
-    - chr1
-    - chr3
-    - chr4
-    - chr5
-    - chr6
-    - chr7
-    - chr8
-    - chr9
-    - chr10
-    - chr11
-    - chr12
-    - chr13
-    - chr14
-    - chr15
-    - chr16
-    - chr18
-    - chr19
-    - chr20
-    - chr21
-    - chr22
-    - chrX
-    - chrY
-    - chrM
+path_genome_folder: /Users/ilya/Projects/quaich/resources/genome/
+path_genome_fasta: /Users/ilya/Projects/quaich/resources/genome/hg38/hg38.fa
+chromsizes: /Users/ilya/Projects/quaich/resources/genome/hg38/hg38_chromsizes.txt
+view: /Users/ilya/Projects/quaich/resources/test_view.txt
+
 
 # Samples file with two columns: sample name ("sample") and path/url with cool file ("file").
 # If it's URL, it will be downloaded. If the file is already downloaded it will not be overwritten.
@@ -75,7 +52,8 @@ saddle:
     distance_limits:
         - 1600000
         - 102400000
-    args: --strength --qrange 0.01 0.99
+    range: "--qrange 0.01 0.99 "
+    extra: "--strength"
 
 pileups:
     do: True
@@ -112,22 +90,20 @@ insulation:
         10000:
             - 50000
             - 100000
-    strength_threshold: 'Li' # Choose between a specific float, Li or Otsu, see https://github.com/open2c/open2c_examples/blob/master/Insulation_and_boundaries.ipynb
-    chunksize: 1000000000
+    extra: '--chunksize 1000000000 --threshold Li' # Choose between a specific float, Li or Otsu, see https://github.com/open2c/open2c_examples/blob/master/Insulation_and_boundaries.ipynb
 
 call_dots:
     methods:
         cooltools:
             do: True
-            max_dist: 10000000
-            fdr: 0.02
-            arguments: ""
+            extra: "--max-loci-separation 10000000 --fdr 0.02"
         chromosight:
             do: True
+            extra: ""
         mustache:
-            do: True
+            do: False
             max_dist: 10000000
-            arguments: "-pt 0.05 -st 0.8"
+            extra: "-pt 0.05 -st 0.8"
     resolutions:
         - 10000
     samples:

resources/test_view.txt

@@ -0,0 +1,4 @@
+chr2 	0 	93139351 	chr2_p
+chr2 	93139351 	242193529 	chr2_q
+chr17	0	24714921	chr17_p
+chr17	24714921	83257441	chr17_q