diff --git a/bin/hicpro_merge_validpairs.sh b/bin/hicpro_merge_validpairs.sh
index 6d455d008ccd4c197a095ded24f956dcefa1c5bc..5f383c534753bf77b05665501453cb9d501bf2c0 100755
--- a/bin/hicpro_merge_validpairs.sh
+++ b/bin/hicpro_merge_validpairs.sh
@@ -25,7 +25,7 @@ if [[ ${rmDup} == 1 ]]; then
 else
     cat ${vpairs} > ${prefix}.allValidPairs
 fi
-    
+      
 echo -e -n "valid_interaction\t" > ${prefix}_allValidPairs.mergestat
 cat ${vpairs} | wc -l >> ${prefix}_allValidPairs.mergestat
 echo -e -n "valid_interaction_rmdup\t" >> ${prefix}_allValidPairs.mergestat
diff --git a/bin/src/cutsite_trimming.cpp b/bin/src/cutsite_trimming.cpp
index ef3fa869cd3bfe5f4e473908224cb42c2b99cbfe..d8ab26f1f522723bf34a8e16ee9cba19f7780da1 100644
--- a/bin/src/cutsite_trimming.cpp
+++ b/bin/src/cutsite_trimming.cpp
@@ -3,11 +3,9 @@
 // Author(s): Nicolas Servant
 // Contact: nicolas.servant@curie.fr
 // This software is distributed without any guarantee under the terms of the BSD-3 licence
-
 // g++ -std=c++0x -o cutsite_trimming cutsite_trimming.cpp
 //./cutsite_trimming -fastq fastq -cutsite AGCTT
 
-
 #include <iostream>     // std::cout
 #include <stdlib.h>
 #include <string.h>
@@ -18,135 +16,131 @@ static const char* prog;
 
 static int usage(int ret=1)
 {
-  std::cerr << "usage: " << prog << " --fastq FASTQFILE --cutsite CUTSITE --out OUTFILE [--rmuntrim] \n";
-  std::cerr << "usage: " << prog << " --help\n";
-  return ret;
+    std::cerr << "usage: " << prog << " --fastq FASTQFILE --cutsite CUTSITE --out OUTFILE [--rmuntrim] \n";
+    std::cerr << "usage: " << prog << " --help\n";
+    return ret;
 }
 
 static int get_options(int argc, char* argv[], std::string& fastqFile,
-                       std::vector<std::string>& cutSites, std::string& output, bool& rmuntrim)
+		       std::vector<std::string>& cutSites, std::string& output, bool& rmuntrim)
 {
-  prog = argv[0];
-  if (argc == 1){
-    exit(usage());
-  }
-  for (int ac = 1; ac < argc; ++ac) {
-    const char* opt = argv[ac];
-    if (*opt == '-') {
-      if (!strcmp(opt, "--fastq")) {
-        fastqFile = std::string(argv[++ac]);
-      } else if (!strcmp(opt, "--cutsite")) {
-
-        std::string cutSitesSequence;
-        cutSitesSequence = std::string(argv[++ac]);
-        size_t pos = cutSitesSequence.find(",");
-        size_t begin = 0;
-        while(pos != std::string::npos){
-          cutSites.push_back(cutSitesSequence.substr(begin, pos - begin));
-          begin = pos + 1;
-          pos = cutSitesSequence.find(",", begin + 1);
-        }
-        cutSites.push_back(cutSitesSequence.substr(begin, pos));
-
+    prog = argv[0];
+    if (argc == 1){
+        exit(usage());
+    }
+    for (int ac = 1; ac < argc; ++ac) {
+      const char* opt = argv[ac];
+      if (*opt == '-') {
+          if (!strcmp(opt, "--fastq")) {
+              fastqFile = std::string(argv[++ac]);
+          }
+	  else if (!strcmp(opt, "--cutsite")) {
+	      std::string cutSitesSequence;
+	      cutSitesSequence = std::string(argv[++ac]);
+	      size_t pos = cutSitesSequence.find(",");
+	      size_t begin = 0;
+	      while(pos != std::string::npos){
+		  cutSites.push_back(cutSitesSequence.substr(begin, pos - begin));
+		  begin = pos + 1;
+		  pos = cutSitesSequence.find(",", begin + 1);
+	      }
+	      cutSites.push_back(cutSitesSequence.substr(begin, pos));
+	  } 
+	  else if (!strcmp(opt, "--out")) {
+	      output = std::string(argv[++ac]);
+	  }
+	  else if (!strcmp(opt, "--rmuntrim")) {
+	      rmuntrim = true;
+	  }
+      }else {
+	  std::cerr << prog << ": unknown option " << opt << std::endl;
+	  return usage();
       } 
-      else if (!strcmp(opt, "--out")) {
-        output = std::string(argv[++ac]);
-      }
-      else if (!strcmp(opt, "--rmuntrim")) {
-        rmuntrim = true;
-      }
-    }else {
-      std::cerr << prog << ": unknown option " << opt << std::endl;
-      return usage();
-    } 
-  }
-  return 0;
+    }
+    return 0;
 }
 
 static int trim_fastq(std::string& fastqFile,
                       std::vector<std::string>& cutSites,
-                      std::string& outFile, bool& rmuntrim)
-{
-
-  int trim_count=0;
-  std::string ID;
-  std::ifstream ifs (fastqFile);
-  std::ofstream ofs (outFile);
-
-  if (ifs.is_open()){
-    while (getline(ifs, ID)) {
-      std::string seq;
-      std::string dummy;
-      std::string qual;
+                      std::string& outFile, bool& rmuntrim){
+    int trim_count=0;
+    std::string ID;
+    std::ifstream ifs (fastqFile);
+    std::ofstream ofs (outFile);
+    
+    if (ifs.is_open()){
+        while (getline(ifs, ID)) {
+	    std::string seq;
+	    std::string dummy;
+	    std::string qual;
       
-      getline(ifs, seq);
-      getline(ifs, dummy);
-      getline(ifs, qual);
-
-      bool find_pos = false;
-      size_t pos = std::string::npos;
-      for (std::vector<std::string>::iterator it = cutSites.begin(); it != cutSites.end(); ++it){
-        size_t tmp_pos = seq.find(*it);
-        if (tmp_pos != std::string::npos) {
-          // If find_pos is alread True, there is a problem (there are two cut
-          // sites in the same read).)
-          if (find_pos == true){
-            if(tmp_pos < pos) {
-              pos = tmp_pos;
-            }
-          } else {
-            find_pos = true;
-            pos = tmp_pos;
-          }
-        }
-      }
+	    getline(ifs, seq);
+	    getline(ifs, dummy);
+	    getline(ifs, qual);
+
+	    bool find_pos = false;
+	    size_t pos = std::string::npos;
+	    for (std::vector<std::string>::iterator it = cutSites.begin(); it != cutSites.end(); ++it){
+	        size_t tmp_pos = seq.find(*it);
+		if (tmp_pos != std::string::npos) {
+		    // If find_pos is alread True, there is a problem (there are two cut
+		    // sites in the same read).)
+		    if (find_pos == true){
+		        if(tmp_pos < pos) {
+			    pos = tmp_pos;
+			}
+		    } else {
+		        find_pos = true;
+			pos = tmp_pos;
+		    }
+		}
+	    }
       
-      if (pos != std::string::npos) {
-        trim_count++;
-        ofs << ID << '\n';
-        ofs << seq.substr(0, pos) << '\n';
-        ofs << "+\n";
-        ofs << qual.substr(0, pos) << '\n';
-      } else {
-        if (!rmuntrim){
-          ofs << ID << '\n';
-          ofs << seq << '\n';
-          ofs << "+\n";
-          ofs << qual << '\n';
-        }
-      }
-      find_pos = false;
+	    if (pos != std::string::npos) {
+	        trim_count++;
+		ofs << ID << '\n';
+		ofs << seq.substr(0, pos) << '\n';
+		ofs << "+\n";
+		ofs << qual.substr(0, pos) << '\n';
+	    } else {
+	        if (!rmuntrim){
+		    ofs << ID << '\n';
+		    ofs << seq << '\n';
+		    ofs << "+\n";
+		    ofs << qual << '\n';
+		}
+	    }
+	    find_pos = false;
+	}
+    }else{
+        std::cerr << "Error : Cannot open file : " << fastqFile;
     }
-  }else{
-    std::cerr << "Error : Cannot open file : " << fastqFile;
-  }
-  return trim_count;
+    return trim_count;
 }
 
 int main(int argc, char* argv[])
 {
-  
-  std::string fastqFile;
-  std::vector<std::string> cutSites;
-  std::string outFile;
-  bool rmuntrim = false;
-
-  int ret = get_options(argc, argv, fastqFile, cutSites, outFile, rmuntrim);
-  printf("##Fastq file: %s\n", fastqFile.c_str());
-  printf("##Restriction sites:\n");
-  for(std::vector<std::string>::iterator it = cutSites.begin(); it != cutSites.end(); ++it){
-    std::cout << *it << std::endl;
-  }
-  printf("##Output File: %s\n", outFile.c_str());
+    std::string fastqFile;
+    std::vector<std::string> cutSites;
+    std::string outFile;
+    bool rmuntrim = false;
+
+    int ret = get_options(argc, argv, fastqFile, cutSites, outFile, rmuntrim);
+    printf("##Fastq file: %s\n", fastqFile.c_str());
+    printf("##Restriction sites:\n");
+    for(std::vector<std::string>::iterator it = cutSites.begin(); it != cutSites.end(); ++it){
+        std::cout << *it << std::endl;
+    }
+    printf("##Output File: %s\n", outFile.c_str());
 
-  if (fastqFile.empty() || cutSites.size() == 0 || outFile.empty()){
-    usage();
-    exit(ret);
-  }
+    if (fastqFile.empty() || cutSites.size() == 0 || outFile.empty()){
+        usage();
+	exit(ret);
+    }
 
-  int trim_count=trim_fastq(fastqFile, cutSites, outFile, rmuntrim);
-  printf("\n##Trimmed reads: %d\n", trim_count);
-  return(0);
+    int trim_count=trim_fastq(fastqFile, cutSites, outFile, rmuntrim);
+    printf("\n##Trimmed reads: %d\n", trim_count);
+    return(0);
  }
 
 
diff --git a/modules/local/cooler/makebins.nf b/modules/local/cooler/makebins.nf
index 49e18db719d8e9b97738d9156b2c6dc3015df6b1..c956a6ae54b80916257a58e1d93c7a7adac98776 100644
--- a/modules/local/cooler/makebins.nf
+++ b/modules/local/cooler/makebins.nf
@@ -1,30 +1,30 @@
 process COOLER_MAKEBINS {
-  tag "${cool_bin}"
-  label 'process_low'
+    tag "${cool_bin}"
+    label 'process_low'
 
-  conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
-      'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+    conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
+      	'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
 
-  input:
-  tuple path(chromsizes), val(cool_bin)
+    input:
+    tuple path(chromsizes), val(cool_bin)
 
-  output:
-  path ("*.bed")       , emit: bed
-  path ("versions.yml"), emit: versions
+    output:
+    path ("*.bed")       , emit: bed
+    path ("versions.yml"), emit: versions
 
-  script:
-  def args = task.ext.args ?: ''
-  """
-  cooler makebins \\
-      $args \\
-      ${chromsizes} \\
-      ${cool_bin} > cooler_bins_${cool_bin}.bed
+    script:
+    def args = task.ext.args ?: ''
+    """
+    cooler makebins \\
+        $args \\
+      	${chromsizes} \\
+      	${cool_bin} > cooler_bins_${cool_bin}.bed
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-      cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/cooltools/eigs-cis.nf b/modules/local/cooltools/eigs-cis.nf
index b65df9a8f9b8e40dcbb3278dc238866c3c25d059..6d77a87ecd1bfc0033a936b4ab92a265f17ed877 100644
--- a/modules/local/cooltools/eigs-cis.nf
+++ b/modules/local/cooltools/eigs-cis.nf
@@ -3,33 +3,33 @@
  */
  
 process CALL_COMPARTMENTS {
-  label 'process_medium'
+    label 'process_medium'
 
-  conda (params.enable_conda ? "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
-      'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
+    conda (params.enable_conda ? "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
+        'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
 
-  input:
-  tuple val(meta), path(cool), val(resolution)
-  path(fasta) 
-  path(chrsize) 
+    input:
+    tuple val(meta), path(cool), val(resolution)
+    path(fasta) 
+    path(chrsize) 
 
-  output:
-  path("*compartments*"), emit: results
-  path("versions.yml"), emit: versions
+    output:
+    path("*compartments*"), emit: results
+    path("versions.yml"), emit: versions
 
-  script:
-  def args = task.ext.args ?: ''
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-  cooltools genome binnify --all-names ${chrsize} ${resolution} > genome_bins.txt
-  cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt 
-  cooltools eigs-cis ${args} -o ${prefix}_compartments ${cool}
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    cooltools genome binnify --all-names ${chrsize} ${resolution} > genome_bins.txt
+    cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt 
+    cooltools eigs-cis ${args} -o ${prefix}_compartments ${cool}
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-      cooltools: \$(cooltools --version 2>&1 | sed 's/cooletools, version //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cooltools: \$(cooltools --version 2>&1 | sed 's/cooletools, version //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index 756579a98695845a099db2d0563c503aaa046867..dc755acbc1b5bce48eb56afb65587f4772a67484 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -3,29 +3,29 @@
  */
  
 process INSULATION {
-  label 'process_medium'
+    label 'process_medium'
 
-  conda (params.enable_conda ? "bioconda::cooltools=0.5.1" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
-      'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }" 
+    conda (params.enable_conda ? "bioconda::cooltools=0.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
+        'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }" 
 
-  input:
-  tuple val(meta), path(cool)
+    input:
+    tuple val(meta), path(cool)
 
-  output:
-  path("*tsv"), emit:results
-  path("versions.yml"), emit:versions
+    output:
+    path("*tsv"), emit:results
+    path("versions.yml"), emit:versions
 
-  script:
-  def args = task.ext.args ?: ''
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-  cooltools insulation ${cool} ${args} > ${prefix}_insulation.tsv
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    cooltools insulation ${cool} ${args} > ${prefix}_insulation.tsv
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-      cooltools: \$(cooltools --version 2>&1 | sed 's/cooltools, version //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cooltools: \$(cooltools --version 2>&1 | sed 's/cooltools, version //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index 2bfca6510f3b74c90de54e4a3d59f83ec8126ebe..093484c24c99f5d3c07071681c5bd3b7808df992 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -3,32 +3,32 @@
  */
  
 process HIC_FIND_TADS {
-  label 'process_medium'
+    label 'process_medium'
 
-  conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
-      'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" 
+    conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
+        'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" 
 
-  input:
-  tuple val(meta), path(cool)
+    input:
+    tuple val(meta), path(cool)
 
-  output:
-  path("*hicfindtads*"), emit:results
-  path("versions.yml"), emit:versions
+    output:
+    path("*hicfindtads*"), emit:results
+    path("versions.yml"), emit:versions
 
-  script:
-  def args = task.ext.args ?: ''
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-  hicFindTADs --matrix ${cool} \
-  	      --outPrefix ${prefix}_hicfindtads \
-	      ${args} \
-	      --numberOfProcessors ${task.cpus}
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    hicFindTADs --matrix ${cool} \
+                --outPrefix ${prefix}_hicfindtads \
+	        ${args} \
+	        --numberOfProcessors ${task.cpus}
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-      hicexplorer: \$(hicFindTADs --version 2>&1 | sed 's/hicFindTADs //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hicexplorer: \$(hicFindTADs --version 2>&1 | sed 's/hicFindTADs //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index ab7754f243f2a5b04d445e68134bd4d49cebe936..a426d12ea6583bcb91bf930454dc449824199ae1 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
@@ -3,31 +3,31 @@
  */
  
 process HIC_PLOT_DIST_VS_COUNTS {
-  label 'process_medium'
+    label 'process_medium'
 
-  conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
-      'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+    conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
+        'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
 
-  input:
-  tuple val(meta), path(cool)
+    input:
+    tuple val(meta), path(cool)
 
-  output:
-  path("*distcount*"), emit:results
-  path("versions.yml"), emit:versions
+    output:
+    path("*distcount*"), emit:results
+    path("versions.yml"), emit:versions
 
-  script:
-  def args = task.ext.args ?: ''
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-  hicPlotDistVsCounts --matrices ${cool} \
-                      --plotFile ${prefix}_distcount.png \
-  		      --outFileData ${prefix}_distcount.txt
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    hicPlotDistVsCounts --matrices ${cool} \
+                        --plotFile ${prefix}_distcount.png \
+                        --outFileData ${prefix}_distcount.txt
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-      hicexplorer: \$(hicPlotDistVsCounts --version 2>&1 | sed 's/hicPlotDistVsCounts //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hicexplorer: \$(hicPlotDistVsCounts --version 2>&1 | sed 's/hicPlotDistVsCounts //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index f0a35fe0ed7d62bac50546002d6f3f747f037ded..3ae9428c041228ec793f2511709df485cafb90df 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/modules/local/hicpro/bowtie2_merge.nf
@@ -1,48 +1,48 @@
 process MERGE_BOWTIE2{
-  tag "$prefix"
-  label 'process_medium'
+    tag "$prefix"
+    label 'process_medium'
   
-  conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-      'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 	
-  input:
-  tuple val(meta), path(bam1), path(bam2) 
+    input:
+    tuple val(meta), path(bam1), path(bam2) 
 
-  output:
-  tuple val(meta), path("${prefix}_bwt2merged.bam"), emit: bam
-  tuple val(meta), path("${prefix}.mapstat"), emit: stats
-  path("versions.yml"), emit: versions
+    output:
+    tuple val(meta), path("${prefix}_bwt2merged.bam"), emit: bam
+    tuple val(meta), path("${prefix}.mapstat"), emit: stats
+    path("versions.yml"), emit: versions
 
-  script:
-  prefix = task.ext.prefix ?: "${meta.id}"
-  tag = meta.mates
-  """
-  samtools merge -@ ${task.cpus} \\
-                 -f ${prefix}_bwt2merged.bam \\
-                  ${bam1} ${bam2}
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    tag = meta.mates
+    """
+    samtools merge -@ ${task.cpus} \\
+                   -f ${prefix}_bwt2merged.bam \\
+                    ${bam1} ${bam2}
 
-  samtools sort -@ ${task.cpus} -m 800M \\
-                -n  \\
-                -o ${prefix}_bwt2merged.sorted.bam \\
-                ${prefix}_bwt2merged.bam
+    samtools sort -@ ${task.cpus} -m 800M \\
+                  -n  \\
+                  -o ${prefix}_bwt2merged.sorted.bam \\
+                  ${prefix}_bwt2merged.bam
 
-  mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
+    mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
 
-  echo "## ${prefix}" > ${prefix}.mapstat
-  echo -n "total_${tag}\t" >> ${prefix}.mapstat
-  samtools view -c ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
-  echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
-  samtools view -c -F 4 ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
-  echo -n "global_${tag}\t" >> ${prefix}.mapstat
-  samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
-  echo -n "local_${tag}\t"  >> ${prefix}.mapstat
-  samtools view -c -F 4 ${bam2} >> ${prefix}.mapstat
+    echo "## ${prefix}" > ${prefix}.mapstat
+    echo -n "total_${tag}\t" >> ${prefix}.mapstat
+    samtools view -c ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+    echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
+    samtools view -c -F 4 ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+    echo -n "global_${tag}\t" >> ${prefix}.mapstat
+    samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+    echo -n "local_${tag}\t"  >> ${prefix}.mapstat
+    samtools view -c -F 4 ${bam2} >> ${prefix}.mapstat
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-  END_VERSIONS
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
   """
 }
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index 322db8165e0e7a7966332059b903f32d862eba2b..e3587c1dde82bb07a52d28899698aea938d916d7 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -1,29 +1,29 @@
 process COMBINE_MATES {
-  tag "$prefix"
-  label 'process_low'
+    tag "$prefix"
+    label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 
-    'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+      'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 
+      'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
  
-  input:
-  tuple val(meta), path(bam)
+    input:
+    tuple val(meta), path(bam)
 
-  output:
-  tuple val(meta), path("*bwt2pairs.bam"), emit:bam
-  tuple val(meta), path("*.pairstat"), optional:true, emit:stats
-  path("versions.yml"), emit: versions
+    output:
+    tuple val(meta), path("*bwt2pairs.bam"), emit:bam
+    tuple val(meta), path("*.pairstat"), optional:true, emit:stats
+    path("versions.yml"), emit: versions
 
-  script:
-  prefix = task.ext.prefix ?: "${meta.id}"
-  def args = task.ext.args ?: ''
-  """
-  mergeSAM.py -f ${bam[0]} -r ${bam[1]} -o ${prefix}_bwt2pairs.bam ${args}
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    """
+    mergeSAM.py -f ${bam[0]} -r ${bam[1]} -o ${prefix}_bwt2pairs.bam ${args}
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+      python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index 20521034f5aa22c0654d89ca0f7a497258e89900..bf0da6fb51e20c1f0d5be37425f22f97bb956883 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/modules/local/hicpro/dnase_mapping_stats.nf
@@ -1,31 +1,31 @@
 process MAPPING_STATS_DNASE {
-  tag "$sample = $bam"
-  label 'process_medium'
+    tag "$sample = $bam"
+    label 'process_medium'
 
-  conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-      'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
 
-  input:
-  tuple val(meta), path(bam) 
+    input:
+    tuple val(meta), path(bam) 
 
-  output:
-  tuple val(meta), path(bam), emit:bam
-  tuple val(meta), path("${prefix}.mapstat"), emit:stats
+    output:
+    tuple val(meta), path(bam), emit:bam
+    tuple val(meta), path("${prefix}.mapstat"), emit:stats
 
-  script:
-  prefix = meta.id + "_" + meta.mates
-  tag = meta.mates
-  """
-  echo "## ${prefix}" > ${prefix}.mapstat
-  echo -n "total_${tag}\t" >> ${prefix}.mapstat
-  samtools view -c ${bam} >> ${prefix}.mapstat
-  echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
-  samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
-  echo -n "global_${tag}\t" >> ${prefix}.mapstat
-  samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
-  echo -n "local_${tag}\t0"  >> ${prefix}.mapstat
-  """
+    script:
+    prefix = meta.id + "_" + meta.mates
+    tag = meta.mates
+    """
+    echo "## ${prefix}" > ${prefix}.mapstat
+    echo -n "total_${tag}\t" >> ${prefix}.mapstat
+    samtools view -c ${bam} >> ${prefix}.mapstat
+    echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
+    samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
+    echo -n "global_${tag}\t" >> ${prefix}.mapstat
+    samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
+    echo -n "local_${tag}\t0"  >> ${prefix}.mapstat
+    """
 }
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index c35e49cb3ccd9bb1790c43e8dfd5558adba46dce..ef56f9d342d35af4d015edf5b95a86ba313d54b5 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -1,27 +1,27 @@
 process GET_RESTRICTION_FRAGMENTS {
-  tag "$res_site"
-  label 'process_low'
+    tag "$res_site"
+    label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::numpy=1.22.3" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-    'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+    conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::numpy=1.22.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+      'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+      'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
-  input:
-  path fasta 
-  val(res_site)
+    input:
+    path fasta 
+    val(res_site)
 
-  output:
-  path "*.bed", emit: results
-  path("versions.yml"), emit: versions
+    output:
+    path "*.bed", emit: results
+    path("versions.yml"), emit: versions
 
-  script:
-  """
-  digest_genome.py -r ${res_site} -o restriction_fragments.bed ${fasta}
+    script:
+    """
+    digest_genome.py -r ${res_site} -o restriction_fragments.bed ${fasta}
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+      python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index 399a9ec7319f72c5e6a953ce1c6d39883d577462..a2bfb84988072d2dd638a624c53d07e636103a49 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -1,37 +1,37 @@
 process GET_VALID_INTERACTION {
-  tag "$meta.id"
-  label 'process_low'
+    tag "$meta.id"
+    label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-    'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+      'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+      'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
-  input:
-  tuple val(meta), path(bam) 
-  path(resfrag)
+    input:
+    tuple val(meta), path(bam) 
+    path(resfrag)
 
-  output:
-  tuple val(meta), path("*.validPairs"), emit:valid_pairs
-  tuple val(meta), path("*.DEPairs"), optional:true, emit:de_pairs
-  tuple val(meta), path("*.SCPairs"), optional: true, emit:sc_pairs
-  tuple val(meta), path("*.REPairs"), optional: true, emit:re_pairs
-  tuple val(meta), path("*.FiltPairs"), optional: true, emit:filt_pairs
-  tuple val(meta), path("*RSstat"), optional: true, emit:stats
-  path("versions.yml"), emit: versions
+    output:
+    tuple val(meta), path("*.validPairs"), emit:valid_pairs
+    tuple val(meta), path("*.DEPairs"), optional:true, emit:de_pairs
+    tuple val(meta), path("*.SCPairs"), optional: true, emit:sc_pairs
+    tuple val(meta), path("*.REPairs"), optional: true, emit:re_pairs
+    tuple val(meta), path("*.FiltPairs"), optional: true, emit:filt_pairs
+    tuple val(meta), path("*RSstat"), optional: true, emit:stats
+    path("versions.yml"), emit: versions
 
-  script:
-  def args = task.ext.args ?: ''
-  """
-  mapped_2hic_fragments.py \\
-    -f ${resfrag} \\
-    -r ${bam} \\
-    --all \\
-    ${args}
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mapped_2hic_fragments.py \\
+      -f ${resfrag} \\
+      -r ${bam} \\
+      --all \\
+      ${args}
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+      python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index dd5b061370c8201149a336e0195e3a429a6ff789..983b85875c169be3351bd1ac3f984795713038ea 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/modules/local/hicpro/get_valid_interaction_dnase.nf
@@ -1,30 +1,30 @@
 process GET_VALID_INTERACTION_DNASE {
-  tag "$meta.id"
-  label 'process_low'
+    tag "$meta.id"
+    label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-    'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+      'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+      'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
  
-  input:
-  tuple val(meta), path(bam) 
+    input:
+    tuple val(meta), path(bam) 
 
-  output:
-  tuple val(meta), path("*.validPairs"), emit:valid_pairs
-  tuple val(meta), path("*RSstat"), optional: true, emit:stats
-  path("versions.yml"), emit: versions
+    output:
+    tuple val(meta), path("*.validPairs"), emit:valid_pairs
+    tuple val(meta), path("*RSstat"), optional: true, emit:stats
+    path("versions.yml"), emit: versions
 
-  script:
-  def args = task.ext.args ?: ''
-  """
-  mapped_2hic_dnase.py \\
-    -r ${bam} \\
-    ${args}
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mapped_2hic_dnase.py \\
+      -r ${bam} \\
+      ${args}
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+      python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index 305bc8713667048d79b76342b2071068c421994a..ddab40eefca7044436c2abc67898d4e9d354686b 100644
--- a/modules/local/hicpro/hicpro2pairs.nf
+++ b/modules/local/hicpro/hicpro2pairs.nf
@@ -1,31 +1,31 @@
 process HICPRO2PAIRS {
-  tag "$meta.id"
-  label 'process_medium'
+    tag "$meta.id"
+    label 'process_medium'
 
-  conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
-      'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
+    conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
+        'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
 
-  input:
-  tuple val(meta), path(vpairs)
-  path chrsize 
+    input:
+    tuple val(meta), path(vpairs)
+    path chrsize 
 
-  output:
-  tuple val(meta), path("*.pairs.gz"), path("*.pairs.gz.px2"), emit: pairs
-  path("versions.yml"), emit: versions
+    output:
+    tuple val(meta), path("*.pairs.gz"), path("*.pairs.gz.px2"), emit: pairs
+    path("versions.yml"), emit: versions
 
-  script:
-  prefix = "${meta.id}"
-  """
-  ##columns: readID chr1 pos1 chr2 pos2 strand1 strand2
-  awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs > ${prefix}_contacts.pairs
-  sort -k2,2 -k4,4 -k3,3n -k5,5n ${prefix}_contacts.pairs | bgzip -c > ${prefix}_contacts.pairs.gz
-  pairix -f ${prefix}_contacts.pairs.gz
+    script:
+    prefix = "${meta.id}"
+    """
+    ##columns: readID chr1 pos1 chr2 pos2 strand1 strand2
+    awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs > ${prefix}_contacts.pairs
+    sort -k2,2 -k4,4 -k3,3n -k5,5n ${prefix}_contacts.pairs | bgzip -c > ${prefix}_contacts.pairs.gz
+    pairix -f ${prefix}_contacts.pairs.gz
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    pairix: \$(echo \$(pairix 2>&1 | grep Version | sed -e 's/Version: //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pairix: \$(echo \$(pairix 2>&1 | grep Version | sed -e 's/Version: //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index 61f3fe2d99594da4c9e0062a34780746bd43ce02..c6cb940759e1bb48416614d2c6f3115865bd782a 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -1,31 +1,31 @@
 process MERGE_STATS {
-  label 'process_low'
+    label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.9" : null)
-   container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-    'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 
+    conda (params.enable_conda ? "conda-forge::python=3.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+      'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+      'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 
 
-  input:
-  tuple val(meta), path(fstat) 
+    input:
+    tuple val(meta), path(fstat) 
 
-  output:
-  path("${meta.id}/"), emit: mqc
-  path("*.{mmapstat,mpairstat,mRSstat}"), emit: stats
-  path("versions.yml"), emit:versions
+    output:
+    path("${meta.id}/"), emit: mqc
+    path("*.{mmapstat,mpairstat,mRSstat}"), emit: stats
+    path("versions.yml"), emit:versions
 
-  script:
-  if ( (fstat =~ /.mapstat/) ){ ext = "${meta.mates}.mmapstat" }
-  if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
-  if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
-  """
-  mkdir -p ${meta.id}
-  merge_statfiles.py -f ${fstat} > ${meta.id}.${ext}
-  cp *${ext} ${meta.id}/
+    script:
+    if ( (fstat =~ /.mapstat/) ){ ext = "${meta.mates}.mmapstat" }
+    if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
+    if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
+    """
+    mkdir -p ${meta.id}
+    merge_statfiles.py -f ${fstat} > ${meta.id}.${ext}
+    cp *${ext} ${meta.id}/
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+      python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index 2ea31823cdb906e178ef9cb79f3959b0848ba8a1..371600c8ff4de2591adb92327d82ba9960e63a9b 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/modules/local/hicpro/merge_valid_interaction.nf
@@ -1,34 +1,34 @@
 process MERGE_VALID_INTERACTION {
-   tag "$prefix"
-   label 'process_highmem'
+    tag "$prefix"
+    label 'process_highmem'
 
-   conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
-   container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"   
+    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+      'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+      'ubuntu:20.04' }"   
 
-   input:
-   tuple val(meta), path(vpairs) 
+    input:
+    tuple val(meta), path(vpairs) 
 
-   output:
-   tuple val(meta), path("*.allValidPairs"), emit: valid_pairs
-   path("${meta.id}/"), emit:mqc
-   path("*mergestat"), emit:stats
-   path("versions.yml"), emit: versions
+    output:
+    tuple val(meta), path("*.allValidPairs"), emit: valid_pairs
+    path("${meta.id}/"), emit:mqc
+    path("*mergestat"), emit:stats
+    path("versions.yml"), emit: versions
 
-   script:
-   prefix = meta.id
-   def args = task.ext.args ?: ''
-   """
-   hicpro_merge_validpairs.sh ${args} -p ${prefix} ${vpairs}
+    script:
+    prefix = meta.id
+    def args = task.ext.args ?: ''
+    """
+    hicpro_merge_validpairs.sh ${args} -p ${prefix} ${vpairs}
 
-   ## For MultiQC
-   mkdir -p ${prefix}
-   cp ${prefix}_allValidPairs.mergestat ${prefix}/
+    ## For MultiQC
+    mkdir -p ${prefix}
+    cp ${prefix}_allValidPairs.mergestat ${prefix}/
 
-   cat <<-END_VERSIONS > versions.yml
-   "${task.process}":
-     sort: \$(echo \$(sort --version 2>&1 | head -1 | awk '{print \$NF}' 2>&1))
-   END_VERSIONS
-   """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+      sort: \$(echo \$(sort --version 2>&1 | head -1 | awk '{print \$NF}' 2>&1))
+    END_VERSIONS
+    """
 }  	
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index 8fc35ec67debd6312a0f03777e25008a55a7d88c..466cd6b12e6daa9bf632a985586405c4991775e3 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -1,32 +1,32 @@
 process ICE_NORMALIZATION{
-  tag "$rmaps"
-  label 'process_highmem'
+    tag "$rmaps"
+    label 'process_highmem'
 
-  conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-    'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+      'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+      'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
  
-  input:
-  tuple val(meta), val(res), path(rmaps), path(bed) 
+    input:
+    tuple val(meta), val(res), path(rmaps), path(bed) 
 
-  output:
-  tuple val(meta), val(res), path("*iced.matrix"), path(bed), emit:maps
-  path ("*.biases"), emit:bias
-  path("versions.yml"), emit: versions
+    output:
+    tuple val(meta), val(res), path("*iced.matrix"), path(bed), emit:maps
+    path ("*.biases"), emit:bias
+    path("versions.yml"), emit: versions
 
-  script:
-  prefix = rmaps.toString() - ~/(\.matrix)?$/
-  """
-  ice --filter_low_counts_perc ${params.ice_filter_low_count_perc} \
-      --results_filename ${prefix}_iced.matrix \
-      --filter_high_counts_perc ${params.ice_filter_high_count_perc} \
-      --max_iter ${params.ice_max_iter} --eps ${params.ice_eps} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${rmaps}
+    script:
+    prefix = rmaps.toString() - ~/(\.matrix)?$/
+    """
+    ice --filter_low_counts_perc ${params.ice_filter_low_count_perc} \
+        --results_filename ${prefix}_iced.matrix \
+        --filter_high_counts_perc ${params.ice_filter_high_count_perc} \
+        --max_iter ${params.ice_max_iter} --eps ${params.ice_eps} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${rmaps}
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
-    iced: \$(python -c "import iced; print(iced.__version__)")
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+      python: \$(echo \$(python --version 2>&1) | sed 's/Python //')
+      iced: \$(python -c "import iced; print(iced.__version__)")
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index 89109afebb9451ca3fde29278fb639442ce610c7..a4ba7d3307cd82a65e5c2e0dc2b4563e74bfef89 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -1,32 +1,32 @@
 process TRIM_READS {
-  tag "$meta.id"
-  label 'process_low'
+    tag "$meta.id"
+    label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
-  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-      'ubuntu:20.04' }"
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
   
-  input:
-  tuple val(meta), path(reads) 
-  val(motif)
+    input:
+    tuple val(meta), path(reads) 
+    val(motif)
 
-  output:
-  tuple val(meta), path("*trimmed.fastq.gz"), emit: fastq
-  path("versions.yml") , emit: versions
+    output:
+    tuple val(meta), path("*trimmed.fastq.gz"), emit: fastq
+    path("versions.yml") , emit: versions
 
-  script:
-  """
-  zcat ${reads} > tmp.fastq
-  cutsite_trimming --fastq tmp.fastq \\
-                   --cutsite ${motif[0]} \\
-                   --out ${reads.simpleName}_trimmed.fastq
-  gzip ${reads.simpleName}_trimmed.fastq
-  /bin/rm -f tmp.fastq
+    script:
+    """
+    zcat ${reads} > tmp.fastq
+    cutsite_trimming --fastq tmp.fastq \\
+                     --cutsite ${motif[0]} \\
+                     --out ${reads.simpleName}_trimmed.fastq
+    gzip ${reads.simpleName}_trimmed.fastq
+    /bin/rm -f tmp.fastq
 
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-      gzip: \$(echo \$(gzip --version 2>&1) | head -1 | cut -d" " -f2)
-  END_VERSIONS
-  """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gzip: \$(echo \$(gzip --version 2>&1) | head -1 | cut -d" " -f2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/trash/bowtie2_end_to_end.nf b/modules/local/trash/bowtie2_end_to_end.nf
deleted file mode 100644
index 8391ac7452a2e152f503aa3f4b18a9c8dd79f92f..0000000000000000000000000000000000000000
--- a/modules/local/trash/bowtie2_end_to_end.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process bowtie2_end_to_end {
-   tag "$sample"
-   label 'process_medium'
-   publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_end2end" : params.outdir },
-              saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
-
-   input:
-   tuple val(sample), path(reads)
-   path index
-
-   output:
-   tuple val(sample), path("${prefix}_unmap.fastq"), emit: unmapped_end_to_end
-   tuple val(sample), path("${prefix}.bam"), emit: end_to_end_bam
-
-   script:
-   prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
-   def bwt2_opts = params.bwt2_opts_end2end
-   if (!params.dnase){
-   """
-   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-   bowtie2 --rg-id BMG --rg SM:${prefix} \\
-	${bwt2_opts} \\
-	-p ${task.cpus} \\
-	-x \${INDEX} \\
-	--un ${prefix}_unmap.fastq \\
- 	-U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
-   """
-   }else{
-   """
-   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-   bowtie2 --rg-id BMG --rg SM:${prefix} \\
-	${bwt2_opts} \\
-	-p ${task.cpus} \\
-	-x \${INDEX} \\
-	--un ${prefix}_unmap.fastq \\
- 	-U ${reads} > ${prefix}.bam
-   """
-   }
-}
diff --git a/modules/local/trash/bowtie2_on_trimmed_reads.nf b/modules/local/trash/bowtie2_on_trimmed_reads.nf
deleted file mode 100644
index a7eb45895bb3ff30d181fadce055be39de4aefbd..0000000000000000000000000000000000000000
--- a/modules/local/trash/bowtie2_on_trimmed_reads.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process bowtie2_on_trimmed_reads {
-   tag "$sample"
-   label 'process_medium'
-   publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_trimmed" : params.outdir },
-   	      saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
-
-   when:
-   !params.dnase
-
-   input:
-   tuple val(sample), path(reads) 
-   path index 
-
-   output:
-   tuple val(sample), path("${prefix}_trimmed.bam"), emit:trimmed_bam
-
-   script:
-   prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
-   """
-   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-   bowtie2 --rg-id BMG --rg SM:${prefix} \\
-           ${params.bwt2_opts_trimmed} \\
-           -p ${task.cpus} \\
-           -x \${INDEX} \\
-           -U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
-   """
-}
diff --git a/modules/local/trash/cooler_balance.nf b/modules/local/trash/cooler_balance.nf
deleted file mode 100644
index 201f06424e74c7ce136dac8cc1a6bae9211d9f80..0000000000000000000000000000000000000000
--- a/modules/local/trash/cooler_balance.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process cooler_balance {
-  tag "$sample - ${res}"
-  label 'process_medium'
-
-  publishDir "${params.outdir}/contact_maps/", mode: 'copy',
-              saveAs: {filename -> filename.endsWith(".cool") ? "norm/cool/$filename" : "norm/txt/$filename"}
-
-  when:
-  !params.skip_balancing
-
-  input:
-  tuple val(sample), val(res), path(cool) 
-  path chrsize 
-
-  output:
-  tuple val(sample), val(res), path("${sample}_${res}_norm.cool"), emit:balanced_cool_maps
-  path("${sample}_${res}_norm.txt"), emit:norm_txt_maps
-
-  script:
-  """
-  cp ${cool} ${sample}_${res}_norm.cool
-  cooler balance ${sample}_${res}_norm.cool -p ${task.cpus} --force
-  cooler dump ${sample}_${res}_norm.cool --balanced --na-rep 0 | awk '{OFS="\t"; print \$1+1,\$2+1,\$4}' > ${sample}_${res}_norm.txt
-  """
-}
diff --git a/modules/local/trash/cooler_raw.nf b/modules/local/trash/cooler_raw.nf
deleted file mode 100644
index 9bc45c5dd6aac47ed2ef92a63f42bd092f000d13..0000000000000000000000000000000000000000
--- a/modules/local/trash/cooler_raw.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process cooler_raw {
-  tag "$sample - ${res}"
-  label 'process_medium'
-
-  publishDir "${params.outdir}/contact_maps/", mode: 'copy',
-              saveAs: {filename -> filename.endsWith(".cool") ? "raw/cool/$filename" : "raw/txt/$filename"}
-
-  input:
-  tuple val(sample), path(contacts), val(res) 
-  path chrsize 
-
-  output:
-  tuple val(sample), val(res), path("*cool"), emit:raw_cool_maps
-  tuple path("*.bed"), path("${sample}_${res}.txt"), emit:raw_txt_maps
-
-  script:
-  """
-  cooler makebins ${chrsize} ${res} > ${sample}_${res}.bed
-  cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 ${sample}_${res}.bed ${contacts} ${sample}_${res}.cool
-  cooler dump ${sample}_${res}.cool | awk '{OFS="\t"; print \$1+1,\$2+1,\$3}' > ${sample}_${res}.txt
-  """
-}
diff --git a/modules/local/trash/cooler_zoomify.nf b/modules/local/trash/cooler_zoomify.nf
deleted file mode 100644
index 1ce68d0288c64359c2a67f7ec85c55cf0a749931..0000000000000000000000000000000000000000
--- a/modules/local/trash/cooler_zoomify.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process cooler_zoomify {
-   tag "$sample"
-   label 'process_medium'
-   publishDir "${params.outdir}/contact_maps/norm/mcool", mode: 'copy'
-
-   when:
-   !params.skip_mcool
-
-   input:
-   tuple val(sample), path(contacts)  
-   path chrsize 
-
-   output:
-   path("*mcool"), emit:mcool_maps
-
-   script:
-   """
-   cooler makebins ${chrsize} ${params.res_zoomify} > bins.bed
-   cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 bins.bed ${contacts} ${sample}.cool
-   cooler zoomify --nproc ${task.cpus} --balance ${sample}.cool
-   """
-}
diff --git a/modules/local/trash/functions.nf b/modules/local/trash/functions.nf
deleted file mode 100644
index da9da093d3f6025e328759a12adc2c1c9ede0d03..0000000000000000000000000000000000000000
--- a/modules/local/trash/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/local/trash/get_chromsize.nf b/modules/local/trash/get_chromsize.nf
deleted file mode 100644
index f6b8c8a913fdf43fe2b7fa1d4544542d57d43ebd..0000000000000000000000000000000000000000
--- a/modules/local/trash/get_chromsize.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-process GET_CHROMSIZE {
-  tag "$fasta"
-  label 'process_low'
-
-  input:
-  path fasta 
-
-  output:
-  path "*.size", emit: results
-
-  script:
-  """
-  samtools faidx ${fasta}
-  cut -f1,2 ${fasta}.fai > chrom.size
-  """
-}
diff --git a/modules/local/trash/get_software_versions.nf b/modules/local/trash/get_software_versions.nf
deleted file mode 100644
index 730316d59f951590334fb60a7ee3f0d29b35cd54..0000000000000000000000000000000000000000
--- a/modules/local/trash/get_software_versions.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-
-process GET_SOFTWARE_VERSIONS {
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
-
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
-
-    cache false
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.tsv"     , emit: tsv
-    path 'software_versions_mqc.yaml', emit: yaml
-
-    script: // This script is bundled with the pipeline, in nf-core/hic/bin/
-    """
-    echo $workflow.manifest.version > pipeline.version.txt
-    echo $workflow.nextflow.version > nextflow.version.txt
-    multiqc --version > v_multiqc.txt
-    scrape_software_versions.py &> software_versions_mqc.yaml
-    """
-}
diff --git a/modules/local/trash/makeBowtie2Index.nf b/modules/local/trash/makeBowtie2Index.nf
deleted file mode 100644
index f38d951949173052c967917e11eeeba6e3f2c9f8..0000000000000000000000000000000000000000
--- a/modules/local/trash/makeBowtie2Index.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process MAKE_BOWTIE2_INDEX {
-    tag "$fasta_base"
-    label 'process_highmem'
-
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
-
-    conda (params.enable_conda ? "bioconda::bowtie2=2.3.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bowtie2:2.3.5--py37he860b03_0"
-    } else {
-        container "quay.io/biocontainers/bowtie2:2.3.5--py37he860b03_0"
-    }
-
-    input:
-        path fasta
-
-        output:
-        path "bowtie2_index", emit: bwt2_index_end2end
-	    path "bowtie2_index", emit: bwt2_index_trim
-
-        script:
-        fasta_base = fasta.toString() - ~/(\.fa)?(\.fasta)?(\.fas)?(\.fsa)?$/
-        """
-        mkdir bowtie2_index
-	bowtie2-build ${fasta} bowtie2_index/${fasta_base}
-	"""
-}
diff --git a/modules/local/trash/output_documentation.nf b/modules/local/trash/output_documentation.nf
deleted file mode 100644
index 7e49c6a79cbfec9b348734c0c05d14794f5003f1..0000000000000000000000000000000000000000
--- a/modules/local/trash/output_documentation.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process output_documentation {
-    publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode
-
-    input:
-    path output_docs 
-    path images 
-
-    output:
-    path 'results_description.html'
-
-    script:
-    """
-    markdown_to_html.py $output_docs -o results_description.html
-    """
-}
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index 3e230f4378fd4d2c98ba1785cf9bea137862f214..9735a49889301692fde334da4403577bfa4313c6 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -70,5 +70,4 @@ def setMetaChunk(row){
     map += [meta, file]
   }
   return map
-}                                                                                                                                                                                                            
-                                                                                                                                                                                                             
+}
\ No newline at end of file