From 4a1b1afc16b27746a97826fb8ea667344e6bc688 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 8 Jun 2020 16:46:53 -0400 Subject: [PATCH 1/2] try out --append_run_id option in viral-core --- pipes/WDL/tasks/tasks_demux.wdl | 1 + requirements-modules.txt | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl index 12f0c425b..36a5b9b04 100644 --- a/pipes/WDL/tasks/tasks_demux.wdl +++ b/pipes/WDL/tasks/tasks_demux.wdl @@ -194,6 +194,7 @@ task illumina_demux { --JVMmemory="$mem_in_mb"m \ $demux_threads \ ${true='--force_gc=true' false="--force_gc=false" forceGC} \ + --append_run_id \ --compression_level=5 \ --loglevel=DEBUG diff --git a/requirements-modules.txt b/requirements-modules.txt index 1bd4ad746..71b30af88 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -1,4 +1,4 @@ -broadinstitute/viral-core=2.1.0 +broadinstitute/viral-core=dp-demux broadinstitute/viral-assemble=2.1.0.0 broadinstitute/viral-classify=2.1.0.0 broadinstitute/viral-phylo=2.1.0.0 From bc66cf837d4789f61309c06fd23f1149da0afc6f Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 9 Jun 2020 12:16:09 -0400 Subject: [PATCH 2/2] upstream merged --- requirements-modules.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-modules.txt b/requirements-modules.txt index 71b30af88..a7e47f6c7 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -1,4 +1,4 @@ -broadinstitute/viral-core=dp-demux +broadinstitute/viral-core=2.1.0-rc3 broadinstitute/viral-assemble=2.1.0.0 broadinstitute/viral-classify=2.1.0.0 broadinstitute/viral-phylo=2.1.0.0