diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..36d4ad2 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,46 @@ +{ + "upload_type": "software", + "description": "This is a GitHub action for releasing to Zenodo without giving webhook admin access", + "title": "Zenodo Release Action", + "creators": [ + { + "affiliation": "The Jackson Laboratory", + "orcid": "0000-0003-1021-8129", + "name": "Michael Lloyd" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Brian Sanderson" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Barry Guglielmo" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Sai Lek" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Peter Fields" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Harshpreet Chandok" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Carolyn Paisie" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Gabriel Rech" + }, + { + "affiliation": "The Jackson Laboratory", + "name": "Anuj Srivastava" + } + ], + "keywords": ["zenodo", "release", "archive"], + "license": "MIT" + } \ No newline at end of file diff --git a/modules/r/annotate_genes_sv.nf b/modules/r/annotate_genes_sv.nf index 75bd9e8..fcb77a8 100644 --- a/modules/r/annotate_genes_sv.nf +++ b/modules/r/annotate_genes_sv.nf @@ -2,8 +2,8 @@ process ANNOTATE_GENES_SV { tag "$sampleID" cpus 1 - memory 8.GB - time '04:00:00' + memory 10.GB + time '10:00:00' errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'} container 'quay.io/jaxcompsci/r-sv_cnv_annotate:4.1.1' @@ -17,7 +17,6 @@ process ANNOTATE_GENES_SV { script: - if (suppl_switch == "main") """ Rscript ${projectDir}/bin/pta/annotate-bedpe-with-genes.r \ diff --git a/modules/r/annotate_genes_sv_mouse.nf b/modules/r/annotate_genes_sv_mouse.nf index 997a144..ba59572 100644 --- a/modules/r/annotate_genes_sv_mouse.nf +++ b/modules/r/annotate_genes_sv_mouse.nf @@ -2,8 +2,8 @@ process ANNOTATE_GENES_SV { tag "$sampleID" cpus 1 - memory 8.GB - time '04:00:00' + memory 10.GB + time '10:00:00' errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'} container 'quay.io/jaxcompsci/r-sv_cnv_annotate:4.1.1' @@ -16,6 +16,7 @@ process ANNOTATE_GENES_SV { tuple val(sampleID), file("*.manta_lumpy_delly_svaba_sv_annotated_genes*.bed"), val(normal_name), val(tumor_name), emit: annot_sv_genes_bedpe script: + if (suppl_switch == "main") """ Rscript ${projectDir}/bin/pta/annotate-bedpe-with-genes-mouse.r \ diff --git a/nextflow.config b/nextflow.config index a7254ab..8fd3687 100644 --- a/nextflow.config +++ b/nextflow.config @@ -45,7 +45,7 @@ manifest { homePage = "https://github.com/TheJacksonLaboratory/cs-nf-pipelines" mainScript = "main.nf" nextflowVersion = "!>=22.04.3" - version = "0.6.0" + version = "0.6.1" author = 'Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Anuj Srivastava. Copyright Jackson Laboratory 2024' }