[MODIF] add containers info

modules/local/dist_decay.nf

-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process dist_decay {
-  tag "$sample"
-  label 'process_medium'
-  publishDir "${params.outdir}/dist_decay", mode: 'copy'
-
-  when:
-  !params.skip_dist_decay
-
-  input:
-  tuple val(sample), val(res), path(maps), val(r) 
-  
-  output:
-  path("*_distcount.txt")
-  path("*.png")
-
-
-  script:
-  """
-  hicPlotDistVsCounts --matrices ${maps} \
-                      --plotFile ${maps.baseName}_distcount.png \
-  		      --outFileData ${maps.baseName}_distcount.txt
-  """
-}

modules/local/hicexplorer/hicFindTADs.nf

@@ -5,6 +5,11 @@
 process HIC_FIND_TADS {
   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' }" 
+
   input:
   tuple val(meta), path(cool)
 

modules/local/hicexplorer/hicPlotDistVsCounts.nf

@@ -5,6 +5,11 @@
 process HIC_PLOT_DIST_VS_COUNTS {
   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' }"
+
   input:
   tuple val(meta), path(cool)
 

modules/local/tads_hicexplorer.nf

-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process tads_hicexplorer {
-  tag "$sample - $res"
-  label 'process_medium'
-  publishDir "${params.outdir}/tads/hicexplorer", mode: 'copy'
-
-  when:
-  !params.skip_tads && params.tads_caller =~ 'hicexplorer'
-
-  input:
-  tuple val(sample), val(res), path(cool), val(r) 
-
-  output:
-  path("*.{bed,bedgraph,gff}"), emit:hicexplorer_tads
-
-  script:
-  """
-  hicFindTADs --matrix ${cool} \
-  	      --outPrefix tad \
-	      --correctForMultipleTesting fdr \
-	      --numberOfProcessors ${task.cpus}
-  """
-}