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Require r-base>=3.5 for RSeqC Conda envs (#654)

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* require conda-forge::r-base>=3.5 for conda-envs

* have same conda requirements for all rseqc submodules
This commit is contained in:
Christian Mertes 2021-08-05 19:59:56 +02:00 committed by GitHub
parent 5de3f2c50e
commit 28b023e6f4
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GPG key ID: 4AEE18F83AFDEB23
7 changed files with 7 additions and 7 deletions
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2
modules/rseqc/bamstat/main.nf
View file

@ -11,7 +11,7 @@ process RSEQC_BAMSTAT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else { } else {

2
modules/rseqc/inferexperiment/main.nf
View file

@ -11,7 +11,7 @@ process RSEQC_INFEREXPERIMENT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else { } else {

2
modules/rseqc/innerdistance/main.nf
View file

@ -11,7 +11,7 @@ process RSEQC_INNERDISTANCE {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else { } else {

2
modules/rseqc/junctionannotation/main.nf
View file

@ -11,7 +11,7 @@ process RSEQC_JUNCTIONANNOTATION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else { } else {

2
modules/rseqc/junctionsaturation/main.nf
View file

@ -11,7 +11,7 @@ process RSEQC_JUNCTIONSATURATION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else { } else {

2
modules/rseqc/readdistribution/main.nf
View file

@ -11,7 +11,7 @@ process RSEQC_READDISTRIBUTION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else { } else {

2
modules/rseqc/readduplication/main.nf
View file

@ -11,7 +11,7 @@ process RSEQC_READDUPLICATION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else { } else {