From 9bae9b41e645cf21d83f1f7e9917b8f27cdd084d Mon Sep 17 00:00:00 2001 From: Tanubrata Dey Date: Fri, 10 Nov 2023 10:19:58 -0500 Subject: [PATCH] Bugfix: Fixes issue with sending email report --- assets/email_template.txt | 5 ----- assets/mskilab-org-nf-jabba_logo.png | Bin 0 -> 21831 bytes assets/mskilab-org-nf-jabba_logo_light.png | Bin 0 -> 21831 bytes conf/base.config | 16 ++++++++-------- modules/local/svaba/main.nf | 2 +- nextflow.config | 16 ++++++++-------- 6 files changed, 17 insertions(+), 22 deletions(-) create mode 100644 assets/mskilab-org-nf-jabba_logo.png create mode 100644 assets/mskilab-org-nf-jabba_logo_light.png diff --git a/assets/email_template.txt b/assets/email_template.txt index ac28653..df03771 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,9 +1,4 @@ ---------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~\\ - |\\ | |__ __ / ` / \\ |__) |__ } { - | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, - 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zie@;LMFVw_)AH*F*dG{UZ+H(dB8-7I3+ri)lpJH(DzVI;4a>!g7Gp42AprnoDGD8l zE}4Y_(_Lun-HrJ!%`gCV+ZmzA2EL_M|?( zOI>2YH}-TzxGf4iGH-E5!8(Z+i9 zn%Ym}vY4O!Q;y&C#GYq4UK1kU_(9J27FWpfKB+$*7XESuJ{9akdDI#vUG2$nd$hx) z>r86T)=?<@-(XbOp}Q2K{3c+Ar^xK*urn$<&$UME?WgC&j}xxTCjX442;z32Iu=cd zmtVq(1%b^LX=Wm%gKLiVo&5+meX;&vBDInl_mpW~kKUTy?n5eZF1wX__Pc-Xcz z;!fL&8~Qt$9_q#|8^^CKi*}!H@#R=Y2Wu0(msJWg4?ibtddCovrkf12UW|cK@!BZL*5;3&r{=~o~Emcfe B`bhu) literal 0 HcmV?d00001 diff --git a/conf/base.config b/conf/base.config index c65d048..f3f6bd1 100644 --- a/conf/base.config +++ b/conf/base.config @@ -37,14 +37,14 @@ process { time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 48.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } } withLabel:process_high { cpus = { check_max( 12 * task.attempt, 'cpus' ) } memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + time = { check_max( 24.h * task.attempt, 'time' ) } } withLabel:process_long { time = { check_max( 20.h * task.attempt, 'time' ) } @@ -97,14 +97,14 @@ process { memory = { check_max( 12.GB * task.attempt, 'memory' ) } } withName: 'SVABA' { - cpus = { check_max( 16 * task.attempt, 'cpus' ) } + cpus = { check_max( 8 * task.attempt, 'cpus' ) } memory = { check_max( 64.GB * task.attempt, 'memory' ) } - time = { check_max( 72.h * task.attempt, 'time' ) } + time = 120.h } withName: 'GRIDSS' { - cpus = { check_max( 16 * task.attempt, 'cpus' ) } + cpus = { check_max( 8 * task.attempt, 'cpus' ) } memory = { check_max( 64.GB * task.attempt, 'memory' ) } - time = { check_max( 72.h * task.attempt, 'time' ) } + time = 120.h } withName: 'GRIDSS_SOMATIC' { cpus = { check_max( 8 * task.attempt, 'cpus' ) } diff --git a/modules/local/svaba/main.nf b/modules/local/svaba/main.nf index cba2c4f..82d76e5 100644 --- a/modules/local/svaba/main.nf +++ b/modules/local/svaba/main.nf @@ -1,7 +1,7 @@ process SVABA { tag "$meta.id" - label 'process_medium' + label 'process_high' conda "bioconda::svaba=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/nextflow.config b/nextflow.config index 3f0f1dc..f52b966 100644 --- a/nextflow.config +++ b/nextflow.config @@ -186,8 +186,8 @@ params { // Config options config_profile_name = null config_profile_description = null - //custom_config_version = 'master' - //custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null @@ -210,11 +210,11 @@ params { includeConfig 'conf/base.config' // Load nf-core custom profiles from different Institutions -//try { -// includeConfig "${params.custom_config_base}/nfcore_custom.config" -//} catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -//} +try { + includeConfig "${params.custom_config_base}/nfcore_custom.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") +} // Load mskilab-org/nf-jabba custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! @@ -373,7 +373,7 @@ dag { manifest { name = 'mskilab-org/nf-jabba' - author = """Tanubrata Dey, Shihab Dider, Joel Rosiene""" + author = """Tanubrata Dey and Shihab Dider""" homePage = 'https://github.com/mskilab-org/nf-jabba' description = """Clinical Core Pipeline for MSkiLab""" mainScript = 'main.nf'