diff --git a/modules.json b/modules.json index f65a0b01..030a54ac 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "affy/justrma": { "branch": "master", - "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", + "git_sha": "02a65e8871e06bac203dec16985fa3de648c99b6", "installed_by": ["modules"] }, "atlasgeneannotationmanipulation/gtf2featureannotation": { diff --git a/modules/nf-core/affy/justrma/environment.yml b/modules/nf-core/affy/justrma/environment.yml index 587ede1e..b0afd895 100644 --- a/modules/nf-core/affy/justrma/environment.yml +++ b/modules/nf-core/affy/justrma/environment.yml @@ -1,3 +1,4 @@ +name: affy_justrma channels: - conda-forge - bioconda diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf index 6dcfdf29..62c71d24 100644 --- a/modules/nf-core/affy/justrma/main.nf +++ b/modules/nf-core/affy/justrma/main.nf @@ -2,7 +2,7 @@ process AFFY_JUSTRMA { tag "$meta.id" label 'process_single' - conda 'modules/nf-core/affy/justrma/environment.yml' + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.78.0--r43ha9d7317_1': 'biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_1' }" diff --git a/modules/nf-core/affy/justrma/meta.yml b/modules/nf-core/affy/justrma/meta.yml index 8b1685fc..cd9b6d6c 100644 --- a/modules/nf-core/affy/justrma/meta.yml +++ b/modules/nf-core/affy/justrma/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://www.bioconductor.org/packages/release/bioc/html/affy.html" tool_dev_url: "https://github.com/Bioconductor/affy" doi: "10.1093/bioinformatics/btg405" - licence: "['LGPL >=2.0']" + licence: ["LGPL >=2.0"] input: - meta: type: map diff --git a/modules/nf-core/affy/justrma/templates/affy_justrma.R b/modules/nf-core/affy/justrma/templates/affy_justrma.R index c632b706..e84b532d 100755 --- a/modules/nf-core/affy/justrma/templates/affy_justrma.R +++ b/modules/nf-core/affy/justrma/templates/affy_justrma.R @@ -69,7 +69,7 @@ install_cdf_db <- function(celfile, annotation = FALSE){ if (annotation){ exts <- c(exts, '.db') } - + options(timeout=600) for (package in paste0(cleaned.cdfName, exts)){ install.packages( package,