From 8739aabbf026ebe1655ed0471dacef9ec4c3cbd0 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 2 Feb 2022 08:00:13 +0100 Subject: [PATCH 1/6] Bump markduplicates by default --- conf/pipeline/eager/eva.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 4c2922d..7ba59fa 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -86,6 +86,7 @@ process { withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + memory = { check_max( 20.GB * task.attempt, 'memory' ) } } withName: library_merge { @@ -247,6 +248,7 @@ profiles { withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + memory = { check_max( 32.GB * task.attempt, 'memory' ) } } withName: library_merge { @@ -412,6 +414,7 @@ profiles { withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + memory = { check_max( 48.GB * task.attempt, 'memory' ) } } withName: library_merge { From 50aafc64101de813ac6740c554214202d76fa611 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 3 Feb 2022 17:03:10 +0100 Subject: [PATCH 2/6] Update eva.config --- conf/pipeline/eager/eva.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 7ba59fa..b512921 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -3,7 +3,7 @@ params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs' + config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs DEV' } // Specific nf-core/eager process configuration From 86a9042eace4dd244ef22e3054bd0c9889cad4e1 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 4 Feb 2022 09:25:01 +0100 Subject: [PATCH 3/6] Update eva.config --- conf/pipeline/eager/eva.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index b512921..c469697 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -134,6 +134,7 @@ process { withName: damageprofiler { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } } withName: circularmapper { @@ -301,6 +302,7 @@ profiles { withName: damageprofiler { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } } withName: circularmapper { @@ -468,6 +470,7 @@ profiles { withName: damageprofiler { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + memory = { check_max( 32.GB * task.attempt, 'memory' ) } } withName: circularmapper { From 81fe720b00322ea60d6d55b23fe645ada3d0968f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 4 Feb 2022 09:31:33 +0100 Subject: [PATCH 4/6] Update eva.config --- conf/pipeline/eager/eva.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index c469697..1530757 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -87,6 +87,7 @@ process { withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } memory = { check_max( 20.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [1, 143,137, 140] ? 'retry' : 'finish' } } withName: library_merge { @@ -250,6 +251,7 @@ profiles { withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } memory = { check_max( 32.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [143,137, 140] ? 'retry' : 'finish' } } withName: library_merge { @@ -417,6 +419,7 @@ profiles { withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 48.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [143,137, 140] ? 'retry' : 'finish' } } withName: library_merge { From aa525c6ebf6d28da67fc442d9d5d2b50d8b0be01 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 6 Feb 2022 09:07:53 +0100 Subject: [PATCH 5/6] Allow exit code 1 retry for all java processes --- conf/pipeline/eager/eva.config | 51 ++++++++++++++++++++++++++++++---- 1 file changed, 46 insertions(+), 5 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 1530757..7b7cef0 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -62,14 +62,17 @@ process { withName: makeSeqDict { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: fastqc { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { @@ -82,12 +85,13 @@ process { withName: dedup { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } memory = { check_max( 20.GB * task.attempt, 'memory' ) } - errorStrategy = { task.exitStatus in [1, 143,137, 140] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: library_merge { @@ -115,35 +119,43 @@ process { withName: maltextract { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: damageprofiler { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circularmapper { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { @@ -153,6 +165,7 @@ process { withName: genotyping_ug { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } } @@ -226,14 +239,17 @@ profiles { withName: makeSeqDict { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: fastqc { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { @@ -246,12 +262,13 @@ profiles { withName: dedup { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } memory = { check_max( 32.GB * task.attempt, 'memory' ) } - errorStrategy = { task.exitStatus in [143,137, 140] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: library_merge { @@ -275,6 +292,7 @@ profiles { clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName:hostremoval_input_fastq { @@ -284,39 +302,48 @@ profiles { withName: maltextract { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: damageprofiler { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circularmapper { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: genotyping_ug { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { @@ -394,14 +421,17 @@ profiles { withName: makeSeqDict { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: fastqc { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: samtools_flagstat { @@ -414,12 +444,13 @@ profiles { withName: dedup { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: markduplicates { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 48.GB * task.attempt, 'memory' ) } - errorStrategy = { task.exitStatus in [143,137, 140] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: library_merge { @@ -449,43 +480,53 @@ profiles { clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 955.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: maltextract { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: multivcfanalyzer { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: mtnucratio { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: vcf2genome { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: qualimap { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: damageprofiler { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } memory = { check_max( 32.GB * task.attempt, 'memory' ) } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circularmapper { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: circulargenerator { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: genotyping_ug { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: preseq { From 8c5a54ac9ff8696c19afe252d774a445ff1c4987 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 6 Feb 2022 19:37:53 +0100 Subject: [PATCH 6/6] Update conf/pipeline/eager/eva.config --- conf/pipeline/eager/eva.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 7b7cef0..d13a71a 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -3,7 +3,7 @@ params { // Specific nf-core/configs params config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs DEV' + config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs' } // Specific nf-core/eager process configuration