Merge pull request #358 from broadinstitute/dp-nextstrain

bugfix for sarscov2_nextstrain

Author: dpark01

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"

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
 

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