From 14aaf7cd27bbc2f514ca2216717486c210f89144 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 28 Apr 2020 15:02:50 -0400 Subject: Update spodgi docker image Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/odgi_to_rdf.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'workflows/pangenome-generate') diff --git a/workflows/pangenome-generate/odgi_to_rdf.cwl b/workflows/pangenome-generate/odgi_to_rdf.cwl index 079d6fb..7f91509 100644 --- a/workflows/pangenome-generate/odgi_to_rdf.cwl +++ b/workflows/pangenome-generate/odgi_to_rdf.cwl @@ -3,7 +3,7 @@ class: CommandLineTool cwlVersion: v1.1 hints: DockerRequirement: - dockerPull: spodgi/spodgi + dockerPull: jerven/spodgi requirements: InlineJavascriptRequirement: {} ShellCommandRequirement: {} -- cgit v1.2.3 From 17300054afc895cacaa372288b511149864da328 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 1 May 2020 10:19:19 -0400 Subject: Set verison tag on spodgi container image Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/odgi_to_rdf.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'workflows/pangenome-generate') diff --git a/workflows/pangenome-generate/odgi_to_rdf.cwl b/workflows/pangenome-generate/odgi_to_rdf.cwl index 7f91509..91abe43 100644 --- a/workflows/pangenome-generate/odgi_to_rdf.cwl +++ b/workflows/pangenome-generate/odgi_to_rdf.cwl @@ -3,7 +3,7 @@ class: CommandLineTool cwlVersion: v1.1 hints: DockerRequirement: - dockerPull: jerven/spodgi + dockerPull: jerven/spodgi:0.0.5 requirements: InlineJavascriptRequirement: {} ShellCommandRequirement: {} -- cgit v1.2.3 From dc6bdac06d06020fa0cb1cc5021e2136c3950a09 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Sun, 3 May 2020 14:57:35 -0400 Subject: Set a RAM requirement on odgi_to_rdf to influence it to run on c5 (because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/odgi_to_rdf.cwl | 2 ++ 1 file changed, 2 insertions(+) (limited to 'workflows/pangenome-generate') diff --git a/workflows/pangenome-generate/odgi_to_rdf.cwl b/workflows/pangenome-generate/odgi_to_rdf.cwl index 91abe43..31ef0c5 100644 --- a/workflows/pangenome-generate/odgi_to_rdf.cwl +++ b/workflows/pangenome-generate/odgi_to_rdf.cwl @@ -7,6 +7,8 @@ hints: requirements: InlineJavascriptRequirement: {} ShellCommandRequirement: {} + ResourceRequirement: + ramMin: $((2 * 1024) + 1) inputs: - id: odgi type: File -- cgit v1.2.3 From 7ae370273020132e7d8bfe7e07591264d6a47960 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 4 May 2020 09:09:46 -0400 Subject: Increase RAM for minimap2 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/minimap2.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'workflows/pangenome-generate') diff --git a/workflows/pangenome-generate/minimap2.cwl b/workflows/pangenome-generate/minimap2.cwl index 42d1dce..bf8eb4c 100644 --- a/workflows/pangenome-generate/minimap2.cwl +++ b/workflows/pangenome-generate/minimap2.cwl @@ -12,7 +12,7 @@ hints: ResourceRequirement: coresMin: 8 coresMax: 32 - ramMin: $(9 * 1024) + ramMin: $(15 * 1024) outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20)) stdout: $(inputs.readsFA.nameroot).paf baseCommand: minimap2 -- cgit v1.2.3 From 84744602734d84972c9220c08afbde1675de6866 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 4 May 2020 13:39:45 -0400 Subject: bump jerven/spodgi image to 0.0.6 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/odgi_to_rdf.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'workflows/pangenome-generate') diff --git a/workflows/pangenome-generate/odgi_to_rdf.cwl b/workflows/pangenome-generate/odgi_to_rdf.cwl index 31ef0c5..e6a279b 100644 --- a/workflows/pangenome-generate/odgi_to_rdf.cwl +++ b/workflows/pangenome-generate/odgi_to_rdf.cwl @@ -3,7 +3,7 @@ class: CommandLineTool cwlVersion: v1.1 hints: DockerRequirement: - dockerPull: jerven/spodgi:0.0.5 + dockerPull: jerven/spodgi:0.0.6 requirements: InlineJavascriptRequirement: {} ShellCommandRequirement: {} -- cgit v1.2.3