[CONTAINERS] add mulled id

modules/local/hicpro/build_contact_maps.nf

 process BUILD_CONTACT_MAPS{
   tag "$meta.id - $res"
   label 'process_highmem'
-  
+
+  conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+  container "${ 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(vpairs), val(res) 
   path chrsize 

modules/local/hicpro/combine_mates.nf

@@ -2,8 +2,11 @@ process COMBINE_MATES {
   tag "$prefix"
   label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.7.6  bioconda::pysam=0.15.4" : null)
-
+  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)
 

modules/local/hicpro/dnase_mapping_stats.nf

@@ -2,6 +2,12 @@ process MAPPING_STATS_DNASE {
   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' }"
+
+
   input:
   tuple val(meta), path(bam) 
 

modules/local/hicpro/get_restriction_fragments.nf

@@ -2,7 +2,10 @@ process GET_RESTRICTION_FRAGMENTS {
   tag "$res_site"
   label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.7.6  conda-forge::numpy=1.18.1" : null)
+  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 

modules/local/hicpro/get_valid_interaction.nf

@@ -2,7 +2,10 @@ process GET_VALID_INTERACTION {
   tag "$meta.id"
   label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.7.6  bioconda::pysam=0.15.4" : 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'}"
 
   input:
   tuple val(meta), path(bam) 

modules/local/hicpro/get_valid_interaction_dnase.nf

@@ -2,8 +2,11 @@ process GET_VALID_INTERACTION_DNASE {
   tag "$meta.id"
   label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.7.6  bioconda::pysam=0.15.4" : 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'}"
+ 
   input:
   tuple val(meta), path(bam) 
 

modules/local/hicpro/merge_stats.nf

 process MERGE_STATS {
   label 'process_low'
 
-  conda (params.enable_conda ? "conda-forge::python=3.7.6" : null)
+  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) 

modules/local/hicpro/run_ice.nf

@@ -2,8 +2,11 @@ process ICE_NORMALIZATION{
   tag "$rmaps"
   label 'process_highmem'
 
-  conda (params.enable_conda ? "conda-forge::python=3.7.6  bioconda::iced=0.5.6" : 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'}"
+ 
   input:
   tuple val(meta), val(res), path(rmaps), path(bed) 
 

modules/local/hicpro/trim_reads.nf

@@ -2,6 +2,11 @@ process TRIM_READS {
   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' }"
+  
   input:
   tuple val(meta), path(reads) 
   val(motif)