From a743fefbd3a83896c89a9174bfd08cd1d55fa531 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Tue, 12 Sep 2023 15:57:03 +0000 Subject: [PATCH 1/7] update docker --- tasks/species_typing/task_tbp_parser.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl index 5fab6d0c6..37da00c72 100644 --- a/tasks/species_typing/task_tbp_parser.wdl +++ b/tasks/species_typing/task_tbp_parser.wdl @@ -13,7 +13,7 @@ task tbp_parser { Int coverage_threshold = 100 Boolean tbp_parser_debug = false - String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.2" + String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.3" Int disk_size = 100 Int memory = 4 Int cpu = 1 From 0065d251514d571cba7dd232d1fe93c5be3e154e Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Tue, 12 Sep 2023 17:55:38 +0000 Subject: [PATCH 2/7] update container --- tasks/species_typing/task_tbp_parser.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl index 37da00c72..2093a8fa2 100644 --- a/tasks/species_typing/task_tbp_parser.wdl +++ b/tasks/species_typing/task_tbp_parser.wdl @@ -13,7 +13,7 @@ task tbp_parser { Int coverage_threshold = 100 Boolean tbp_parser_debug = false - String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.3" + String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.4" Int disk_size = 100 Int memory = 4 Int cpu = 1 From 2f9e80a2464396152340590ec20d4e34499528fc Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Wed, 13 Sep 2023 15:26:10 +0000 Subject: [PATCH 3/7] update docker --- tasks/species_typing/task_tbp_parser.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl index 2093a8fa2..f86302275 100644 --- a/tasks/species_typing/task_tbp_parser.wdl +++ b/tasks/species_typing/task_tbp_parser.wdl @@ -13,7 +13,7 @@ task tbp_parser { Int coverage_threshold = 100 Boolean tbp_parser_debug = false - String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.4" + String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.5" Int disk_size = 100 Int memory = 4 Int cpu = 1 From 5227d77f7e95097f5b3e5d66048cdf2bbdc61c67 Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Thu, 14 Sep 2023 06:57:00 -0700 Subject: [PATCH 4/7] Add preemptible, shorter version string (#185) --- tasks/species_typing/task_tbp_parser.wdl | 3 ++- tasks/species_typing/task_tbprofiler.wdl | 5 +++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl index f86302275..2f5824979 100644 --- a/tasks/species_typing/task_tbp_parser.wdl +++ b/tasks/species_typing/task_tbp_parser.wdl @@ -50,6 +50,7 @@ task tbp_parser { cpu: cpu disks: "local-disk " + disk_size + " SSD" disk: disk_size + " GB" - maxRetries: 3 + maxRetries: 3 + preemptible: 1 } } \ No newline at end of file diff --git a/tasks/species_typing/task_tbprofiler.wdl b/tasks/species_typing/task_tbprofiler.wdl index a3a881243..7b9cad530 100644 --- a/tasks/species_typing/task_tbprofiler.wdl +++ b/tasks/species_typing/task_tbprofiler.wdl @@ -22,7 +22,7 @@ task tbprofiler { date | tee DATE # Print and save version - tb-profiler version > VERSION && sed -i -e 's/^/TBProfiler version /' VERSION + tb-profiler version > VERSION && sed -i -e 's/TBProfiler version //' VERSION && sed -n -i '$p' VERSION if [ -z "~{read2}" ] ; then INPUT_READS="-1 ~{read1}" @@ -119,6 +119,7 @@ task tbprofiler { cpu: cpu disks: "local-disk " + disk_size + " SSD" disk: disk_size + " GB" - maxRetries: 3 + maxRetries: 3 + preemptible: 1 } } \ No newline at end of file From 8fcfefa47339e0fd40a268d8dabf69f86453f317 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Fri, 15 Sep 2023 14:53:15 +0000 Subject: [PATCH 5/7] update docker --- tasks/species_typing/task_tbp_parser.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl index 2f5824979..20a0a19d2 100644 --- a/tasks/species_typing/task_tbp_parser.wdl +++ b/tasks/species_typing/task_tbp_parser.wdl @@ -13,7 +13,7 @@ task tbp_parser { Int coverage_threshold = 100 Boolean tbp_parser_debug = false - String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.5" + String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.6" Int disk_size = 100 Int memory = 4 Int cpu = 1 From 7d00801bd2756922f7771dcbd54f4153e5cc6bb1 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Fri, 15 Sep 2023 16:02:24 +0000 Subject: [PATCH 6/7] update docker --- tasks/species_typing/task_tbp_parser.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl index 20a0a19d2..aecf88b8b 100644 --- a/tasks/species_typing/task_tbp_parser.wdl +++ b/tasks/species_typing/task_tbp_parser.wdl @@ -13,7 +13,7 @@ task tbp_parser { Int coverage_threshold = 100 Boolean tbp_parser_debug = false - String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.6" + String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.7" Int disk_size = 100 Int memory = 4 Int cpu = 1 From 51ddccdbc96936329dbbf3bf3ef1f1e3904b287f Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Fri, 15 Sep 2023 16:56:18 +0000 Subject: [PATCH 7/7] update docker --- tasks/species_typing/task_tbp_parser.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/species_typing/task_tbp_parser.wdl b/tasks/species_typing/task_tbp_parser.wdl index aecf88b8b..4f82830a8 100644 --- a/tasks/species_typing/task_tbp_parser.wdl +++ b/tasks/species_typing/task_tbp_parser.wdl @@ -13,7 +13,7 @@ task tbp_parser { Int coverage_threshold = 100 Boolean tbp_parser_debug = false - String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.7" + String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.8" Int disk_size = 100 Int memory = 4 Int cpu = 1