Merge pull request #432 from broadinstitute/pangolin

update pangolin docker to 4.1.1-pdata-1.11
broadinstitute · Jul 5, 2022 · 920df81 · 920df81
2 parents 68d1288 + 21e9389
commit 920df81
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Showing 4 changed files with 21 additions and 9 deletions.
diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl
@@ -97,6 +97,7 @@ task nextclade_many_samples {
         File?        virus_properties
         String?      dataset_name
         String       basename
+        File?        genome_ids_setdefault_blank
         String       docker = "nextstrain/nextclade:2.0.0"
     }
     command <<<
@@ -141,12 +142,22 @@ task nextclade_many_samples {
         # transpose table
         import codecs, csv, json
         out_maps = {'clade':{}, 'aaSubstitutions':{}, 'aaDeletions':{}}
-        with codecs.open('~{basename}.nextclade.tsv', 'r', encoding='utf-8') as inf:
-            with codecs.open('IDLIST', 'w', encoding='utf-8') as outf_ids:
+        with codecs.open('IDLIST', 'w', encoding='utf-8') as outf_ids:
+            # parse entries from output tsv into jsons
+            with codecs.open('~{basename}.nextclade.tsv', 'r', encoding='utf-8') as inf:
                 for row in csv.DictReader(inf, delimiter='\t'):
-                    for k in ('clade','aaSubstitutions','aaDeletions'):
+                    for k in out_maps.keys():
                         out_maps[k][row['seqName']] = row[k]
                     outf_ids.write(row['seqName']+'\n')
+            # fill empty values for anything not mentioned by output tsv
+            with codecs.open("~{default='/dev/null' genome_ids_setdefault_blank}", 'r', encoding='utf-8') as inf:
+                for line in inf:
+                    seqName = line.strip()
+                    if seqName and (seqName not in out_maps['clade']):
+                        for k in out_maps.keys():
+                            out_maps[k][seqName] = ''
+                        outf_ids.write(seqName+'\n')
+
         with codecs.open('NEXTCLADE_CLADE.json', 'w', encoding='utf-8') as outf:
             json.dump(out_maps['clade'], outf)
         with codecs.open('NEXTCLADE_AASUBS.json', 'w', encoding='utf-8') as outf:

diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl
@@ -10,7 +10,7 @@ task pangolin_one_sample {
         Float?  max_ambig
         String? analysis_mode
         Boolean update_dbs_now=false
-        String  docker = "quay.io/staphb/pangolin:4.0.6-pdata-1.9"
+        String  docker = "quay.io/staphb/pangolin:4.1.1-pdata-1.11"
     }
     String basename = basename(genome_fasta, ".fasta")
     command <<<
@@ -91,7 +91,7 @@ task pangolin_many_samples {
         String?      analysis_mode
         Boolean      update_dbs_now=false
         String       basename
-        String       docker = "quay.io/staphb/pangolin:4.0.6-pdata-1.9"
+        String       docker = "quay.io/staphb/pangolin:4.1.1-pdata-1.11"
     }
     command <<<
         set -ex

diff --git a/pipes/WDL/workflows/sarscov2_batch_relineage.wdl b/pipes/WDL/workflows/sarscov2_batch_relineage.wdl
@@ -38,9 +38,10 @@ workflow sarscov2_batch_relineage {
 
     call nextstrain.nextclade_many_samples {
         input:
-            genome_fastas = [filter_sequences_by_length.filtered_fasta],
-            basename      = "nextclade-~{flowcell_id}",
-            dataset_name  = "sars-cov-2"
+            genome_fastas               = [filter_sequences_by_length.filtered_fasta],
+            genome_ids_setdefault_blank = fasta_to_ids.ids_txt,
+            basename                    = "nextclade-~{flowcell_id}",
+            dataset_name                = "sars-cov-2"
     }
 
     call sarscov2.pangolin_many_samples {

diff --git a/requirements-modules.txt b/requirements-modules.txt
@@ -7,5 +7,5 @@ broadinstitute/beast-beagle-cuda=1.10.5pre
 broadinstitute/ncbi-tools=2.10.7.10
 nextstrain/base=build-20211012T204409Z
 andersenlabapps/ivar=1.3.1
-quay.io/staphb/pangolin=4.0.6-pdata-1.9
+quay.io/staphb/pangolin=4.1.1-pdata-1.11
 nextstrain/nextclade=2.0.0