From b77883708a64277935db8f265ecd37761ee3fd4b Mon Sep 17 00:00:00 2001 From: Danny Park Date: Thu, 19 Aug 2021 15:34:24 -0400 Subject: [PATCH 1/2] bugfix for sarscov2_nextstrain: augur refine and augur ancestral were using unmasked aligned fasta inputs instead of the masked inputs like the augur tree step --- pipes/WDL/workflows/sarscov2_nextstrain.wdl | 5 +++-- pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/pipes/WDL/workflows/sarscov2_nextstrain.wdl b/pipes/WDL/workflows/sarscov2_nextstrain.wdl index 0adace1ee..cd7fe00b8 100644 --- a/pipes/WDL/workflows/sarscov2_nextstrain.wdl +++ b/pipes/WDL/workflows/sarscov2_nextstrain.wdl @@ -124,7 +124,7 @@ workflow sarscov2_nextstrain { call nextstrain.refine_augur_tree { input: raw_tree = draft_augur_tree.aligned_tree, - msa_or_vcf = subsample.subsampled_msa, + msa_or_vcf = augur_mask_sites.masked_sequences, metadata = derived_cols.derived_metadata, root = tree_root_seq_id } @@ -153,7 +153,7 @@ workflow sarscov2_nextstrain { call nextstrain.ancestral_tree { input: tree = refine_augur_tree.tree_refined, - msa_or_vcf = subsample.subsampled_msa + msa_or_vcf = augur_mask_sites.masked_sequences } call nextstrain.translate_augur_tree { @@ -196,6 +196,7 @@ workflow sarscov2_nextstrain { File metadata_merged = derived_cols.derived_metadata File keep_list = fasta_to_ids.ids_txt File subsampled_sequences = subsample.subsampled_msa + File masked_alignment = augur_mask_sites.masked_sequences Int sequences_kept = subsample.sequences_out Map[String, Int] counts_by_group = subsample.counts_by_group diff --git a/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl b/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl index a0d620553..ccd4cdd64 100644 --- a/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl +++ b/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl @@ -111,7 +111,7 @@ workflow sarscov2_nextstrain_aligned_input { call nextstrain.refine_augur_tree { input: raw_tree = draft_augur_tree.aligned_tree, - msa_or_vcf = subsample.subsampled_msa, + msa_or_vcf = augur_mask_sites.masked_sequences, metadata = derived_cols.derived_metadata, root = tree_root_seq_id } @@ -140,7 +140,7 @@ workflow sarscov2_nextstrain_aligned_input { call nextstrain.ancestral_tree { input: tree = refine_augur_tree.tree_refined, - msa_or_vcf = subsample.subsampled_msa + msa_or_vcf = augur_mask_sites.masked_sequences } call nextstrain.translate_augur_tree { @@ -181,6 +181,7 @@ workflow sarscov2_nextstrain_aligned_input { File metadata_merged = derived_cols.derived_metadata File keep_list = fasta_to_ids.ids_txt File subsampled_sequences = subsample.subsampled_msa + File masked_alignment = augur_mask_sites.masked_sequences Int sequences_kept = subsample.sequences_out Map[String, Int] counts_by_group = subsample.counts_by_group From 40f4af42cc424db37b04b280f4fddbb364000d10 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Thu, 19 Aug 2021 23:15:12 -0400 Subject: [PATCH 2/2] bump augur export ram --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index cb43e30ce..73bacc389 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1588,7 +1588,7 @@ task export_auspice_json { } runtime { docker: docker - memory: "7 GB" + memory: "13 GB" cpu : 2 disks: "local-disk 100 HDD" dx_instance_type: "mem1_ssd1_v2_x2"