Update README

Author: robomics

README.md

@@ -1,6 +1,6 @@
 # Synopsis
 
-This repository contains the source code and input data used for the data analysis and modeling for Deterioration of multi-level 3D genome organization during breast cancer progression (preprint available soon).
+This repository contains the source code and input data used for the data analysis and modeling for: Deterioration of multi-level 3D genome organization during breast cancer progression (preprint available soon).
 
 Input data download and subsequent analyses are automated using Nextflow and Singularity/Apptainer.
 

bin/plotting/plot_tads_higlass.ipynb

@@ -38,4 +38,3 @@ singularity {
     autoMounts = true
     runOptions = "-B $TMPDIR:/tmp --env TMPDIR=/tmp --cleanenv"
 }
-

configs/base_hovig.config

@@ -4,7 +4,7 @@
 
 process {
     cpus          = 1
-    cache         = 'deep'
+    // cache         = 'deep'
 
     // Process-specific resource requirements
     withLabel:process_low {

configs/base_linux.config

@@ -9,11 +9,11 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 RUN if [ -z "$CONTAINER_VERSION" ]; then echo "Missing CONTAINER_VERSION --build-arg" && exit 1; fi
 
-RUN micromamba install -y                         \
-               -c conda-forge                     \
-               -c bioconda                        \
-               procps-ng                          \
-               ucsc-bedgraphtobigwig              \
+RUN micromamba install -y                   \
+               -c conda-forge               \
+               -c bioconda                  \
+               procps-ng                    \
+               ucsc-bedgraphtobigwig        \
                "macs2=${CONTAINER_VERSION}" \
 && micromamba clean --all -y
 

containers/macs2__v2.2.9.1.Dockerfile

@@ -139,12 +139,12 @@ index deb6a5c..32315f7 100644
  #include <limits>
  #include <stdexcept>
 +#include <string>
- 
+
  #include <sstream>
- 
+
 @@ -191,11 +192,11 @@ int main(int argc, char** argv) {
    //model.buildHashMap();
- 
+
    MCMC mcmc(model);
 -  bool success;
 -  uint Niter=args.nIter;
@@ -153,9 +153,9 @@ index deb6a5c..32315f7 100644
    double temp=maxTemp;
 +  bool success;
 +  (void)success; // [[maybe_unused]]
- 
+
    uint verbosity = (args.verbose == 0) ? args.nIter+1 : args.verbose;
- 
+
 @@ -212,7 +213,7 @@ cerr << "0 " << model.getLossScore() << endl;
      assert(success);
      if (i % verbosity == 0) {
@@ -199,8 +199,8 @@ index 4e738b5..358a089 100644
    virtual Move randomize(Chromosome&, ENG&) = 0;
 +  virtual ~Randomizer() noexcept = default;
  };
- 
- 
+
+
 diff --git a/src/Util.h b/src/Util.h
 index 0116f65..5875dd9 100644
 --- a/src/Util.h
@@ -212,5 +212,5 @@ index 0116f65..5875dd9 100644
 -    const char* what(){return "Unacceptable move!";}
 +    virtual const char* what() const noexcept {return "Unacceptable move!";}
    };
- 
+
  }

containers/patches/chrom3d.patch

@@ -8,7 +8,7 @@ index defd88d..0f6d223 100644
      scales = np.ones(len(chrom_ids))
 +    variances = np.full_like(scales, np.nan)
      n_bins = len(bias)
- 
+
      for cid, lo, hi in zip(chrom_ids, chrom_offsets[:-1], chrom_offsets[1:]):
 @@ -142,6 +143,7 @@ def _balance_cisonly(
          plo, phi = bin1_offsets[lo], bin1_offsets[hi]
@@ -25,14 +25,14 @@ index defd88d..0f6d223 100644
 +        variances[cid] = var
          if rescale_marginals:
              bias[lo:hi] /= np.sqrt(scale)
- 
+
 -    return bias, scales, var
 +    return bias, scales, variances
- 
- 
+
+
  def _balance_transonly(
 @@ -337,7 +340,7 @@ def balance_cooler(
- 
+
      """
      # Divide the number of elements into non-overlapping chunks
 -    nnz = clr.info["nnz"]
@@ -42,7 +42,7 @@ index defd88d..0f6d223 100644
          spans = [(0, nnz)]
 @@ -353,7 +356,7 @@ def balance_cooler(
          base_filters.append(partial(_zero_diags, ignore_diags))
- 
+
      # Initialize the bias weights
 -    n_bins = clr.info["nbins"]
 +    n_bins = int(clr.info["nbins"])
@@ -69,7 +69,7 @@ index ca3627d..68a0242 100644
 @@ -100,7 +100,7 @@ def interactive(ax, c, row_chrom, col_chrom, field, balanced, scale):  # pragma:
          im.set_extent(extent)
          ax.figure.canvas.draw_idle()
- 
+
 -    binsize = c.info["bin-size"]
 +    binsize = int(c.info["bin-size"])
      row_chrom_len = c.chromsizes[row_chrom]
@@ -80,7 +80,7 @@ index daa4f61..de9ef6e 100644
 --- cooler/parallel.py
 +++ cooler/parallel.py
 @@ -268,5 +268,5 @@ class chunkgetter:
- 
+
  def split(clr, map=map, chunksize=10_000_000, spans=None, **kwargs):
      if spans is None:
 -        spans = partition(0, clr.info["nnz"], chunksize)