From 1b0be3ad06eee6f0a8da7b8dfec2ad8693631d9c Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 19 Dec 2022 16:16:10 +0100
Subject: [PATCH] [MODULE] replace cooler local module by nfcore module
---
modules/local/cooler/balance.nf | 35 ----------------------------
modules/local/cooler/cload.nf | 39 --------------------------------
modules/local/cooler/dump.nf | 35 ----------------------------
modules/local/cooler/makebins.nf | 30 ------------------------
4 files changed, 139 deletions(-)
delete mode 100644 modules/local/cooler/balance.nf
delete mode 100644 modules/local/cooler/cload.nf
delete mode 100644 modules/local/cooler/dump.nf
delete mode 100644 modules/local/cooler/makebins.nf
diff --git a/modules/local/cooler/balance.nf b/modules/local/cooler/balance.nf
deleted file mode 100644
index d03959a..0000000
--- a/modules/local/cooler/balance.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-process COOLER_BALANCE {
- tag "$meta.id"
- label 'process_high'
-
- conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
- container "${ 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 val(meta), path(cool), val(resolution)
-
- output:
- tuple val(meta), path("${prefix}.${extension}"), emit: cool
- path "versions.yml" , emit: versions
-
- script:
- def args = task.ext.args ?: ''
- prefix = task.ext.prefix ?: "${cool.baseName}_balanced"
- suffix = resolution ? "::$resolution" : ""
- extension = cool.getExtension()
- """
- cooler balance \\
- $args \\
- -p ${task.cpus} \\
- ${cool}${suffix}
-
- cp ${cool} ${prefix}.${extension}
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
- END_VERSIONS
- """
-}
diff --git a/modules/local/cooler/cload.nf b/modules/local/cooler/cload.nf
deleted file mode 100644
index 2dd29b7..0000000
--- a/modules/local/cooler/cload.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-process COOLER_CLOAD {
- tag "$meta.id"
- label 'process_high'
-
- conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
-
- input:
- tuple val(meta), path(pairs), path(index), val(cool_bin)
- path chromsizes
-
- output:
- tuple val(meta), path("*.cool"), val(cool_bin), emit: cool
- path "versions.yml" , emit: versions
-
- when:
- task.ext.when == null || task.ext.when
-
- script:
- def args = task.ext.args ?: ''
- def prefix = task.ext.prefix ?: "${meta.id}"
- def nproc = args.contains('pairix') || args.contains('tabix')? "--nproc $task.cpus" : ''
-
- """
- cooler cload \\
- $args \\
- $nproc \\
- ${chromsizes}:${cool_bin} \\
- $pairs \\
- ${prefix}.${cool_bin}.cool
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
- END_VERSIONS
- """
-}
diff --git a/modules/local/cooler/dump.nf b/modules/local/cooler/dump.nf
deleted file mode 100644
index 0c01c8d..0000000
--- a/modules/local/cooler/dump.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-process COOLER_DUMP {
- tag "$meta.id"
- label 'process_high'
-
- conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
-
- input:
- tuple val(meta), path(cool), val(resolution)
-
- output:
- tuple val(meta), path("*.bedpe"), emit: bedpe
- path "versions.yml" , emit: versions
-
- when:
- task.ext.when == null || task.ext.when
-
- script:
- def args = task.ext.args ?: ''
- def prefix = task.ext.prefix ?: "${meta.id}"
- def suffix = resolution ? "::$resolution" : ""
- """
- cooler dump \\
- $args \\
- -o ${prefix}.bedpe \\
- $cool$suffix
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
- END_VERSIONS
- """
-}
diff --git a/modules/local/cooler/makebins.nf b/modules/local/cooler/makebins.nf
deleted file mode 100644
index 09147d4..0000000
--- a/modules/local/cooler/makebins.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-process COOLER_MAKEBINS {
- tag "${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' }"
-
- input:
- tuple path(chromsizes), val(cool_bin)
-
- 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
-
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
- END_VERSIONS
- """
-}
--
GitLab