From 4d6df6a5c8ffad4a4bf9b09334e1acf68ef4b348 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 6 May 2022 12:11:30 +0200
Subject: [PATCH] [CONTAINERS] add mulled id
---
modules/local/hicpro/build_contact_maps.nf | 7 ++++++-
modules/local/hicpro/combine_mates.nf | 7 +++++--
modules/local/hicpro/dnase_mapping_stats.nf | 6 ++++++
modules/local/hicpro/get_restriction_fragments.nf | 5 ++++-
modules/local/hicpro/get_valid_interaction.nf | 5 ++++-
modules/local/hicpro/get_valid_interaction_dnase.nf | 7 +++++--
modules/local/hicpro/merge_stats.nf | 5 ++++-
modules/local/hicpro/run_ice.nf | 7 +++++--
modules/local/hicpro/trim_reads.nf | 5 +++++
9 files changed, 44 insertions(+), 10 deletions(-)
diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf
index 0a9a35b..1ba3550 100644
--- a/modules/local/hicpro/build_contact_maps.nf
+++ b/modules/local/hicpro/build_contact_maps.nf
@@ -1,7 +1,12 @@
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
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index 00a88c8..322db81 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/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)
diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index aa78141..2052103 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/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)
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index 63b08f2..c35e49c 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/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
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index 1d271a4..4942eac 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/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)
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index c43bf3f..f34433b 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/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)
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index c79afbc..61f3fe2 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -1,7 +1,10 @@
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), path(fstat)
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index ef7da65..8fc35ec 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -2,8 +2,11 @@ process ICE_NORMALIZATION{
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+
input:
tuple val(meta), val(res), path(rmaps), path(bed)
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index 19edff1..b54811f 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -2,6 +2,11 @@ process TRIM_READS {
tag "$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)
--
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