From 53208dfbe380104a03b29467300aa47587c9f53c Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Thu, 5 May 2022 20:33:20 +0200
Subject: [PATCH] [MODIF] add containers info
---
modules/local/dist_decay.nf | 29 -------------------
modules/local/hicexplorer/hicFindTADs.nf | 5 ++++
.../local/hicexplorer/hicPlotDistVsCounts.nf | 5 ++++
modules/local/tads_hicexplorer.nf | 28 ------------------
4 files changed, 10 insertions(+), 57 deletions(-)
delete mode 100644 modules/local/dist_decay.nf
delete mode 100644 modules/local/tads_hicexplorer.nf
diff --git a/modules/local/dist_decay.nf b/modules/local/dist_decay.nf
deleted file mode 100644
index e5bc660..0000000
--- a/modules/local/dist_decay.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-// 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 ${maps.baseName}_distcount.txt
- """
-}
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index 676e8e7..2bfca65 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -5,6 +5,11 @@
process HIC_FIND_TADS {
label 'process_medium'
+ conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
+ container "${ 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)
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index 41041eb..ab7754f 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
+ 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+
input:
tuple val(meta), path(cool)
diff --git a/modules/local/tads_hicexplorer.nf b/modules/local/tads_hicexplorer.nf
deleted file mode 100644
index 0bb4088..0000000
--- a/modules/local/tads_hicexplorer.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-process tads_hicexplorer {
- tag "$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}
- """
-}
--
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