From afe935c2d04c3950b01feb0613f508164c652005 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 15 Apr 2022 15:27:41 +0200 Subject: [PATCH 01/10] include stub profile --- conf/hasta.config | 22 +++++++++++++++++++--- conf/pipeline/raredisease/hasta.config | 21 +++++++++++++++++++-- 2 files changed, 38 insertions(+), 5 deletions(-) diff --git a/conf/hasta.config b/conf/hasta.config index c5dd5e4..d12cc40 100644 --- a/conf/hasta.config +++ b/conf/hasta.config @@ -15,19 +15,35 @@ singularity { params { max_memory = 180.GB max_cpus = 36 - max_time = 336.h + max_time = 336.h } process { executor = 'slurm' - clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" } + clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" } +} + +params { + max_memory = 180.GB + max_cpus = 36 + max_time = 336.h } profiles { - dev_prio { + stub_prio { params { priority = 'development' clusterOptions = "--qos=low" + max_memory = 1.GB + max_cpus = 1 + max_time = 1.h + } + } + + dev_prio { + params { + priority = 'development' + clusterOptions = "--qos=low" } } diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 96e3332..9d6e0c9 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -1,5 +1,5 @@ process { - + withName:'PICARD_MARKDUPLICATES' { memory = { check_max( 90.GB * task.attempt, 'memory' ) } } @@ -7,4 +7,21 @@ process { cpus = { check_max( 16 * task.attempt, 'cpus' ) } memory = { check_max( 80.GB * task.attempt, 'memory' ) } } -} \ No newline at end of file + withname: BCFTOOLS_VIEW { + if (params.genome == 'GRCh37') { + ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' + } else if (params.genome == 'GRCh38') { + ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegenAF > 0.40"' + } + publishDir = [ + enabled: false, + ] + } + +} + +params { + + sentieon_install_dir = '/home/proj/bin/sentieon/sentieon-genomics-202010.02/bin' + +} From 6fad232232c5fff70fc849092f7f9ba1374c6f39 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 19 Apr 2022 11:27:35 +0200 Subject: [PATCH 02/10] sentieon env variable --- conf/pipeline/raredisease/hasta.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 9d6e0c9..7beb3ba 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -22,6 +22,6 @@ process { params { - sentieon_install_dir = '/home/proj/bin/sentieon/sentieon-genomics-202010.02/bin' + sentieon_install_dir = "$SENTIEON_INSTALL_DIR/bin" } From 32207a240273e86665c8ed072b3ec3ee358fdde1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 19 Apr 2022 11:42:05 +0200 Subject: [PATCH 03/10] update path so that the sentieon version is explicit --- conf/pipeline/raredisease/hasta.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 7beb3ba..56c1a97 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -22,6 +22,6 @@ process { params { - sentieon_install_dir = "$SENTIEON_INSTALL_DIR/bin" + sentieon_install_dir = "$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" } From d39bec05dcf0016d720ea73744283150c9e410c1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 19 Apr 2022 13:21:51 +0200 Subject: [PATCH 04/10] fix typo --- conf/pipeline/raredisease/hasta.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 56c1a97..4e00c56 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -7,11 +7,11 @@ process { cpus = { check_max( 16 * task.attempt, 'cpus' ) } memory = { check_max( 80.GB * task.attempt, 'memory' ) } } - withname: BCFTOOLS_VIEW { + withName: BCFTOOLS_VIEW { if (params.genome == 'GRCh37') { ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' } else if (params.genome == 'GRCh38') { - ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegenAF > 0.40"' + ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"' } publishDir = [ enabled: false, From 3e3e2be04beda1477a26b53f94d9165aee9147d2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 22 Apr 2022 00:09:29 +0200 Subject: [PATCH 05/10] remove duplicate entries --- conf/hasta.config | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/conf/hasta.config b/conf/hasta.config index d12cc40..03e61b8 100644 --- a/conf/hasta.config +++ b/conf/hasta.config @@ -23,18 +23,12 @@ process { clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" } } -params { - max_memory = 180.GB - max_cpus = 36 - max_time = 336.h -} - profiles { stub_prio { params { priority = 'development' clusterOptions = "--qos=low" - max_memory = 1.GB + max_memory = 6.GB max_cpus = 1 max_time = 1.h } From 447b3ee05d5a696a39d222d1b1c703a2e77725a8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 22 Apr 2022 11:03:09 +0200 Subject: [PATCH 06/10] add beforescript for sentieon --- conf/pipeline/raredisease/hasta.config | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 4e00c56..18c7bab 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -7,6 +7,12 @@ process { cpus = { check_max( 16 * task.attempt, 'cpus' ) } memory = { check_max( 80.GB * task.attempt, 'memory' ) } } + withLabel:'sentieon' { + beforeScript = { [ + "export SENTIEON_LICENSE=\$(echo -e \$SENTIEON_LICENSE_BASE64 | base64 -d)", + "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" + ].join(";") } + } withName: BCFTOOLS_VIEW { if (params.genome == 'GRCh37') { ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' @@ -20,8 +26,3 @@ process { } -params { - - sentieon_install_dir = "$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" - -} From 9da85209f234e10d8e84b11d9bd7ee39a2a2fc4f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 22 Apr 2022 11:05:56 +0200 Subject: [PATCH 07/10] change bcftools output format --- conf/pipeline/raredisease/hasta.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 18c7bab..1359522 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -15,9 +15,9 @@ process { } withName: BCFTOOLS_VIEW { if (params.genome == 'GRCh37') { - ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' + ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' } else if (params.genome == 'GRCh38') { - ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"' + ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"' } publishDir = [ enabled: false, From 40c965c76b612925d69087976644c1c0243ba46c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 29 Apr 2022 00:20:57 +0200 Subject: [PATCH 08/10] fix sentieon errors --- conf/pipeline/raredisease/hasta.config | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 1359522..fb4d94a 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -8,10 +8,7 @@ process { memory = { check_max( 80.GB * task.attempt, 'memory' ) } } withLabel:'sentieon' { - beforeScript = { [ - "export SENTIEON_LICENSE=\$(echo -e \$SENTIEON_LICENSE_BASE64 | base64 -d)", - "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" - ].join(";") } + beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" } } withName: BCFTOOLS_VIEW { if (params.genome == 'GRCh37') { From 1c942759ea9e30822181fb9d854744f102c62e18 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 18 Aug 2022 15:52:31 +0200 Subject: [PATCH 09/10] update sentieon --- conf/pipeline/raredisease/hasta.config | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index fb4d94a..1bec159 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -8,7 +8,14 @@ process { memory = { check_max( 80.GB * task.attempt, 'memory' ) } } withLabel:'sentieon' { - beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" } + beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" } + } + // Java memory fixes + withName:'QUALIMAP_BAMQC' { + clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" } + } + withName:'PICARD_MARKDUPLICATES' { + clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" } } withName: BCFTOOLS_VIEW { if (params.genome == 'GRCh37') { From dd63dee7aa6422354311dcf4a55945ad18d01f1d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 18 Aug 2022 15:56:41 +0200 Subject: [PATCH 10/10] update conf --- conf/pipeline/raredisease/hasta.config | 7 ------- 1 file changed, 7 deletions(-) diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 1bec159..d655bf7 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -10,13 +10,6 @@ process { withLabel:'sentieon' { beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" } } - // Java memory fixes - withName:'QUALIMAP_BAMQC' { - clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" } - } - withName:'PICARD_MARKDUPLICATES' { - clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" } - } withName: BCFTOOLS_VIEW { if (params.genome == 'GRCh37') { ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'