feat: cooltools wrappers (#519)

* First try cooltools insulation wrapper

* Fix env formatting?

* Fix test workflow

* add comments to snakefile

* Add expected, add view to insulation

* Add eigenvector wrappers

* Add forgotten tests

* Add saddle, fix so tests pass

* Remove file path for saddle

* Add pileup, small fixes

* FIx pileup meta

* Add genome binnify and gc

* Remove unnecessary empty view assignment

Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>

* Remove unnecessary empty view assignment

Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>

* Remove unnecessary empty view assignment

Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>

* Requested fixes

* Small fixes in gc and binnify wrappers

* Simplify environment

* Requested changes - env, view input, all outputs

* Add example with track for eigs

* Remove extra newline?

* Move note to notes

* Suggested changes, and better wrapper for saddle

* Fix for no fig in saddle

* Only get fig once

* Removed unnecessary else

* Removed format

* Add cooltools dots wrapper

* Changed pinned version

* Remove unnecessary param

* Remove unnecessary import

* Add small test file for dots

* Move view description to input

* Update bio/cooltools/dots/environment.yaml

* Update bio/cooltools/dots/test/Snakefile

Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/cooltools/dots/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - scikit-learn==1.0 # doesn't work with 1.1
+  - cooltools =0.5

bio/cooltools/dots/meta.yaml

@@ -0,0 +1,19 @@
+name: cooltools dots
+description: Calculate cis eigenvectors for a resolution in an .mcool file
+url: https://github.com/open2c/cooltools
+authors:
+  - Ilya Flyamer
+input:
+  - a multiresolution cooler file (.mcool)
+  - an expected file
+  - (optional) view, a bed-style file with region coordinates and names to use for analysis
+output:
+  - >
+    A .bedpe file with coordinates of detected dots.
+    Can have a {resolution} wildcard that specifies the resolution for the analysis,
+    then it doesn't need to be specified as a parameter.
+params:
+  resolution: >
+    Optional, can be instead specified as a wildcard in the output
+  extra: Any additional arguments to pass
+notes:

bio/cooltools/dots/test/Snakefile

@@ -0,0 +1,15 @@
+
+rule cooltools_dots:
+    input:
+        cooler="small_test.mcool",  ## Multiresolution cooler file
+        expected="test_expected.tsv",  ## Expected file
+        view="test_view.txt",  ## File with the region names and coordinates
+    output:
+        "HFF_{resolution,[0-9]+}.dots.bedpe",
+    params:
+        extra="",  ## Add extra parameters
+    threads: 4
+    log:
+        "logs/HFF_{resolution}_dots.log",
+    wrapper:
+        "master/bio/cooltools/dots"

bio/cooltools/dots/test/test_view.txt

@@ -0,0 +1 @@
+chr17	0	24714921	chr17_p

bio/cooltools/dots/wrapper.py

@@ -0,0 +1,34 @@
+__author__ = "Ilya Flyamer"
+__copyright__ = "Copyright 2022, Ilya Flyamer"
+__email__ = "flyamer@gmail.com"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+## Extract arguments
+view = snakemake.input.get("view", "")
+if view:
+    view = f"--view {view}"
+
+expected = snakemake.input.get("expected", "")
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+resolution = snakemake.params.get(
+    "resolution", snakemake.wildcards.get("resolution", 0)
+)
+if not resolution:
+    raise ValueError(
+        "Please specify ressolution either as a wildcard or as a parameter"
+    )
+
+shell(
+    "(cooltools dots"
+    " {snakemake.input.cooler}::resolutions/{resolution} "
+    " {expected} "
+    " {view} "
+    " -p {snakemake.threads} "
+    " {extra} "
+    " -o {snakemake.output}) {log}"
+)

bio/cooltools/eigs_cis/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - defaults
+  - bioconda
+dependencies:
+  - ucsc-bedgraphtobigwig
+  - cooltools =0.5

bio/cooltools/eigs_cis/meta.yaml

@@ -0,0 +1,22 @@
+name: cooltools eigs_cis
+description: Calculate cis eigenvectors for a resolution in an .mcool file
+url: https://github.com/open2c/cooltools
+authors:
+  - Ilya Flyamer
+input:
+  - a multiresolution cooler file (.mcool)
+  - (optional) phasing track file
+  - (optional) view, a bed-style file with region coordinates and names to use for analysis
+output:
+  vecs: A .tsv file with values of cis eigenvectors at each bin.
+  lams: A file with eigenvalues
+  bigwig: A .bigwig file for visualization of the first eigenvector
+params:
+  resolution: >
+    Optional, can be instead specified as a wildcard in the output
+  track_col_name: >
+    Name of the column in the track file to use
+  extra: Any additional arguments to pass
+notes:
+    - Output files can have a {resolution} wildcard that specifies the resolution for
+      the analysis, then it doesn't need to be specified as a parameter.

bio/cooltools/eigs_cis/test/Snakefile

@@ -0,0 +1,17 @@
+rule cooltools_eigs_cis:
+    input:
+        cooler="CN.mm9.1000kb.mcool",  ## Multiresolution cooler file
+        view="mm9_view.txt",  ## File with the region names and coordinates
+        track="mm9_1000000_gc.bed",
+    output:
+        vecs="CN_{resolution,[0-9]+}.cis.vecs.tsv",
+        lam="CN_{resolution,[0-9]+}.cis.lam.tsv",
+        bigwig="CN_{resolution,[0-9]+}.cis.bw",
+    params:
+        ## Add optional parameters
+        track_col_name="GC",
+        extra="",
+    log:
+        "logs/CN_{resolution}_cis_eigs.log",
+    wrapper:
+        "master/bio/cooltools/eigs_cis"