From 51c15f76789c9c9b3b68f285ac7c23b0596dc41a Mon Sep 17 00:00:00 2001 From: William Rowell Date: Wed, 18 Oct 2023 10:53:09 -0700 Subject: [PATCH 1/6] Fix for concat_vcf for miniwdl. Link all inputs into a single directory so that vcfs and indices are together. --- workflows/sample_analysis/sample_analysis.wdl | 4 +++- workflows/wdl-common | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/workflows/sample_analysis/sample_analysis.wdl b/workflows/sample_analysis/sample_analysis.wdl index 990e3b91..41621cf4 100644 --- a/workflows/sample_analysis/sample_analysis.wdl +++ b/workflows/sample_analysis/sample_analysis.wdl @@ -68,7 +68,9 @@ workflow sample_analysis { runtime_attributes = default_runtime_attributes } - scatter (region_set in pbsv_splits) { + scatter (shard_index in range(length(pbsv_splits))) { + Array[String] region_set = pbsv_splits[shard_index] + call PbsvCall.pbsv_call { input: sample_id = sample.sample_id, diff --git a/workflows/wdl-common b/workflows/wdl-common index 8a2f30e9..4c120734 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 8a2f30e9ad3b392b9502b829abb091fff205898b +Subproject commit 4c120734d077a801f281c72f2dfcff3ed5517e59 From 66f486b52b6d9a1c4fc6b0c0acb6c6076aa8e7f5 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 18:10:27 +0000 Subject: [PATCH 2/6] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index d38a2661..134e3b92 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -419,7 +419,7 @@ "tasks": { "pbsv_call": { "key": "pbsv_call", - "digest": "77yon47d6t327ocrw6bed3dccyq5t3va", + "digest": "o5xv2etbm2j4s32d5xs626xj6sp2ykmj", "tests": [ { "inputs": { From c4f26ab7bbb3ff9b78bb79bc8bf7bb7455f0747c Mon Sep 17 00:00:00 2001 From: William Rowell Date: Wed, 18 Oct 2023 11:32:28 -0700 Subject: [PATCH 3/6] pass shard index to pbsv_call --- workflows/sample_analysis/sample_analysis.wdl | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/sample_analysis/sample_analysis.wdl b/workflows/sample_analysis/sample_analysis.wdl index 41621cf4..1f4f1a8d 100644 --- a/workflows/sample_analysis/sample_analysis.wdl +++ b/workflows/sample_analysis/sample_analysis.wdl @@ -78,6 +78,7 @@ workflow sample_analysis { reference = reference.fasta.data, reference_index = reference.fasta.data_index, reference_name = reference.name, + shard_index = shard_index, regions = region_set, runtime_attributes = default_runtime_attributes } From e6aee541597e8b4ed53c8ff65d7a7f654a9225dc Mon Sep 17 00:00:00 2001 From: William Rowell Date: Wed, 18 Oct 2023 11:46:54 -0700 Subject: [PATCH 4/6] Find all concat_vcf inputs. --- workflows/wdl-common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/wdl-common b/workflows/wdl-common index 4c120734..d08984b2 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 4c120734d077a801f281c72f2dfcff3ed5517e59 +Subproject commit d08984b223fbc3fdab511cdfe0e6ca7987a41603 From 863c6eece91424d8ca99af9ffe77964b51777257 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 18:55:59 +0000 Subject: [PATCH 5/6] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 134e3b92..f5620547 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -457,7 +457,7 @@ "tasks": { "concat_vcf": { "key": "concat_vcf", - "digest": "ntfiawmetxbdacle2l7mpu5tkz2jmtz2", + "digest": "xkyvutmrg3gz6zgabdmwcjvcbwrbwwp7", "tests": [ { "inputs": { From b447c8e28e966b10e3b350a1cf3bd4ad315c182b Mon Sep 17 00:00:00 2001 From: William Rowell Date: Wed, 18 Oct 2023 14:45:12 -0700 Subject: [PATCH 6/6] Update cohort_analysis pbsv_call to use shard_index. --- workflows/cohort_analysis/cohort_analysis.wdl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/workflows/cohort_analysis/cohort_analysis.wdl b/workflows/cohort_analysis/cohort_analysis.wdl index 4ebeba6f..8a9970b5 100644 --- a/workflows/cohort_analysis/cohort_analysis.wdl +++ b/workflows/cohort_analysis/cohort_analysis.wdl @@ -32,7 +32,9 @@ workflow cohort_analysis { File gvcf_index = gvcf_object.data_index } - scatter (region_set in pbsv_splits) { + scatter (shard_index in range(length(pbsv_splits))) { + Array[String] region_set = pbsv_splits[shard_index] + call PbsvCall.pbsv_call { input: sample_id = cohort_id + ".joint", @@ -41,6 +43,7 @@ workflow cohort_analysis { reference = reference.fasta.data, reference_index = reference.fasta.data_index, reference_name = reference.name, + shard_index = shard_index, regions = region_set, mem_gb = pbsv_call_mem_gb, runtime_attributes = default_runtime_attributes