From 9fef6214d111c1e87ea307593f8bf6adc576fd48 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 28 Feb 2022 19:26:37 +0100
Subject: [PATCH] [MODIF] add hicexplorer
---
modules/local/hicexplorer/hicFindTADs.nf | 29 +++++++++++++++++++
.../local/hicexplorer/hicPlotDistVsCounts.nf | 28 ++++++++++++++++++
2 files changed, 57 insertions(+)
create mode 100644 modules/local/hicexplorer/hicFindTADs.nf
create mode 100644 modules/local/hicexplorer/hicPlotDistVsCounts.nf
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
new file mode 100644
index 0000000..676e8e7
--- /dev/null
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -0,0 +1,29 @@
+/*
+ * hicexplorer - hicFindTADs
+ */
+
+process HIC_FIND_TADS {
+ label 'process_medium'
+
+ input:
+ tuple val(meta), path(cool)
+
+ 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 ${task.cpus}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${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
new file mode 100644
index 0000000..41041eb
--- /dev/null
+++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
@@ -0,0 +1,28 @@
+/*
+ * hicexplorer - hicPlotDistVsCounts
+ */
+
+process HIC_PLOT_DIST_VS_COUNTS {
+ label 'process_medium'
+
+ input:
+ tuple val(meta), path(cool)
+
+ 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 ${prefix}_distcount.txt
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ hicexplorer: \$(hicPlotDistVsCounts --version 2>&1 | sed 's/hicPlotDistVsCounts //')
+ END_VERSIONS
+ """
+}
--
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