Merge remote-tracking branch 'origin/master' into test

ncbi · Apr 14, 2022 · dc6014d · dc6014d
2 parents 1b8d71c + 656113d
commit dc6014d
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Showing 6 changed files with 14 additions and 18 deletions.
diff --git a/bacterial_orthology/wf_bacterial_orthology.cwl b/bacterial_orthology/wf_bacterial_orthology.cwl
@@ -101,8 +101,6 @@ steps:
       affinity: 
           default: subject
       asn_cache: asn_cache
-      align_filter: 
-          default: 'score>0 && pct_identity_gapopen_only > 35' 
       allow_intersection: 
           default: true
       comp_based_stats:   
@@ -114,27 +112,23 @@ steps:
       delay:
           default: 0
       evalue: 
-          default: 0.1
+          default: 0.001
       max_batch_length: 
           default: 10000
       max_jobs: 
           default: 1
       max_target_seqs: 
-          default: 50
+          default: 250
       no_merge: 
           default: false
       nogenbank: 
           default: true
       ofmt: 
           default: asn-binary
       seg: 
-          default:  '30 2.2 2.5'
-      soft_masking:
-          default: 'yes'
+          default:  'no'
       threshold: 
           default: 21
-      top_by_score: 
-          default: 10
       word_size: 
           default: 6
       taxid: taxid

diff --git a/progs/cluster_blastp_wnode.cwl b/progs/cluster_blastp_wnode.cwl
@@ -27,7 +27,7 @@ inputs:
       prefix: -asn-cache
       itemSeparator: ","
   align_filter: 
-    type: string
+    type: string?
     inputBinding:
       prefix: -align_filter
   allow_intersection:

diff --git a/progs/find_orthologs.cwl b/progs/find_orthologs.cwl
@@ -32,6 +32,8 @@ inputs:
   check_exome:
     type: boolean
     default: true
+    inputBinding:
+      prefix: -check_exome
   o_orthologs:
     type: string?
     default: orthologs.rpt
@@ -55,4 +57,4 @@ outputs:
     type: File
     outputBinding: 
       glob: $(inputs.o_orthologs)  
-
+
diff --git a/task_types/tt_blastp_wnode_naming.cwl b/task_types/tt_blastp_wnode_naming.cwl
@@ -16,7 +16,7 @@ inputs:
   asn_cache: Directory[]
   max_batch_length: int
   nogenbank: boolean
-  align_filter: string
+  align_filter: string?
   allow_intersection: boolean
   comp_based_stats: string # F/T
   compart: boolean
@@ -28,9 +28,9 @@ inputs:
   no_merge: boolean
   ofmt: string
   seg: string
-  soft_masking: string
+  soft_masking: string?
   threshold: int
-  top_by_score: int
+  top_by_score: int?
   word_size: int
   ids: File[]
   batch-size: int?

diff --git a/task_types/tt_cluster_and_qdump.cwl b/task_types/tt_cluster_and_qdump.cwl
@@ -19,7 +19,7 @@ inputs:
   proteins: File
   asn_cache: Directory[]
   nogenbank: boolean
-  align_filter: string
+  align_filter: string?
   allow_intersection: boolean
   comp_based_stats: string # F/T
   compart: boolean
@@ -31,9 +31,9 @@ inputs:
   no_merge: boolean
   ofmt: string
   seg: string
-  soft_masking: string
+  soft_masking: string?
   threshold: int
-  top_by_score: int
+  top_by_score: int?
   word_size: int
   short_protein_threshold: int?
 

diff --git a/wf_common.cwl b/wf_common.cwl
@@ -570,7 +570,7 @@ steps:
       taxon_db: passdata/taxon_db
       gc_cache: passdata/gc_cache
       asn_cache: 
-        source: [passdata/uniColl_nuc_cache]
+        source: [passdata/uniColl_nuc_cache, genomic_source/asncache]
         linkMerge: merge_flattened
       blast_hits_cache: blast_hits_cache_data_split_dir/blast_hits_cache
       genus_list: genus_list_file2ints/values