added Public Domain notice; NOJIRA

README.md

@@ -8,3 +8,25 @@ Genome annotation is a multi-level process that includes prediction of protein-c
 NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume.  NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.
 
 This implementation is intended to be accessible outside of the NCBI network and availible to all users. It is based on CWL and Docker containers. This is a work in progress and not currently functional.
+
+## Public Domain notice
+
+National Center for Biotechnology Information.
+
+This software is a "United States Government Work" under the terms of the
+United States Copyright Act.  It was written as part of the authors'
+official duties as United States Government employees and thus cannot
+be copyrighted.  This software is freely available to the public for
+use. The National Library of Medicine and the U.S. Government have not
+placed any restriction on its use or reproduction.
+
+Although all reasonable efforts have been taken to ensure the accuracy
+and reliability of the software and data, the NLM and the U.S.
+Government do not and cannot warrant the performance or results that
+may be obtained by using this software or data. The NLM and the U.S.
+Government disclaim all warranties, express or implied, including
+warranties of performance, merchantability or fitness for any
+particular purpose.
+
+Please cite NCBI in any work or product based on this material.
+

bacterial_kmer/.gitignore

@@ -0,0 +1,6 @@
+input/*
+output/*
+*.asn
+*.xml
+pgap.*
+output.txt

bacterial_kmer/input_wf_bacterial_kmer.yaml

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+Extract_Kmers_From_Input___entry: # take this from Prepare Unannotated Sequences/out/sequences.asn
+    class: File
+    location: input/sequences.asn
+gencoll_asn: # take this from Create Assembly From Sequences
+    class: File
+    location: input/gencoll.asn
+asn_cache:
+    class: Directory
+    location: input/sequence_cache
+ref_assembly_taxid: 243273
+    # Mycoplasma genitalium G37, corresponding to the input gencoll_asn file.
+ANI_cutoff: 
+    class: File
+    location: input/ANI_cutoff.xml
+kmer_cache_path:
+    class: Directory
+    location: input/kmer-cache-minhash

bacterial_kmer/wf_bacterial_kmer.cwl

@@ -0,0 +1,171 @@
+#!/usr/bin/env cwl-runner
+label: bacterial_kmer
+cwlVersion: v1.0
+class: Workflow 
+requirements: 
+    - class: SubworkflowFeatureRequirement    
+    - class: MultipleInputFeatureRequirement
+hints:
+  DockerRequirement:
+    dockerPull: ncbi/gpdev:latest
+
+inputs:
+  # kmer_minhash_tarball: File # tarball of all reference minhashes. For Mycoplasma genitalium, there are 8K files, in total 1G
+  Extract_Kmers_From_Input___entry: File
+  gencoll_asn: File
+  asn_cache: Directory
+  kmer_cache_path: Directory
+  ref_assembly_taxid: int
+  ANI_cutoff: File
+outputs:
+  Identify_Top_N_ANI_annot:
+    type: File
+    outputSource: Identify_Top_N_ANI/annot
+  Identify_Top_N_ANI_top:
+    type: File
+    outputSource: Identify_Top_N_ANI/top
+  Extract_Top_Assemblies___tax_report:
+    type: File
+    outputSource: Extract_Top_Assemblies/tax_report
+steps:
+# order manually set to match the order of display on the GPC graph for the plane in the buildrun
+  Get_Reference_Assemblies:
+    run: ../task_types/tt_bact_get_kmer_reference.cwl
+    in: []
+    out: [gc_id_list]
+  Query_Kmer_Cache:
+    run: ../task_types/tt_kmer_cache_retrieve.cwl
+    in:
+      gc_id_list: Get_Reference_Assemblies/gc_id_list
+      kmer_cache_path: kmer_cache_path
+    out: [new_gc_id_list, out_kmer_file_list, out_kmer_cache_path]
+  Extract_Kmer_List:
+    run: ../task_types/tt_kmer_gc_extract_wnode.cwl
+    in:
+      new_gc_id_list: Query_Kmer_Cache/new_gc_id_list
+      asn_cache: asn_cache
+    out: [out_kmer_file_list]
+  Store_in_Kmer_Cache:
+    run: ../task_types/tt_kmer_cache_store.cwl
+    in:
+      kmer_cache_path: Query_Kmer_Cache/out_kmer_cache_path
+      kmer_file_list: Extract_Kmer_List/out_kmer_file_list
+    out: [out_kmer_file_list]
+  Extract_Kmers_From_Input:
+    run: ../task_types/tt_kmer_seq_entry_extract_wnode.cwl
+    in:
+      entry: Extract_Kmers_From_Input___entry
+      kmer_file_list: 
+        source: [Query_Kmer_Cache/out_kmer_file_list, Store_in_Kmer_Cache/out_kmer_file_list]
+        linkMerge: merge_flattened
+      asn_cache: asn_cache
+    out: [out_kmer_file_list]
+  Compare_Kmer:
+    run: ../task_types/tt_kmer_ref_compare_wnode.cwl
+    in:
+      kmer_file_list: Extract_Kmers_From_Input/out_kmer_file_list
+      ref_kmer_file_list:  
+        source: [Query_Kmer_Cache/out_kmer_file_list, Store_in_Kmer_Cache/out_kmer_file_list]
+        linkMerge: merge_flattened
+      dist_method:
+        default: minhash
+      minhash_signature:
+        default: minhash
+      score_method:
+        default: boolean
+    out: [distances]
+  Identify_Top_N:
+    run: ../task_types/tt_kmer_top_n.cwl
+    in:
+      distances: Compare_Kmer/distances
+    out: [matches, top_distances]
+  Compare_Kmer__Pairwise_:
+    run: ../task_types/tt_kmer_compare_wnode.cwl
+    in:
+      kmer_file_list: 
+        source: [Extract_Kmers_From_Input/out_kmer_file_list, Identify_Top_N/matches]
+        linkMerge: merge_flattened
+      dist_method:
+        default: minhash
+      minhash_signature:
+        default: minhash
+      score_method:
+        default: boolean
+    out: [distances]
+  Extract_Top_Assemblies:
+    run: ../task_types/tt_kmer_top_n_extract.cwl
+    in:
+      top_distances: Identify_Top_N/top_distances
+      ref_assembly_taxid: ref_assembly_taxid
+    out: [tax_report, gc_id_list]
+  Build_Kmer_Tree:
+    run: ../task_types/tt_kmer_build_tree.cwl
+    in:
+        distances: Compare_Kmer__Pairwise_/distances
+        sort:
+            default: leaf-count-ascending
+        no_merge:
+            default: true
+        skip_markup:
+            default: true
+    out: [tree]
+  Get_Top_Assemblies_GenColl_ASN:
+    run: ../task_types/tt_gcaccess_from_list.cwl
+    in:
+      gc_id_list: Extract_Top_Assemblies/gc_id_list
+    out: [gencoll_asn]
+  Extract_Input_GenColl_IDs:
+    run: ../task_types/tt_extract_gencoll_ids.cwl
+    in: 
+        assemblies: gencoll_asn
+    out: [gc_id_list]
+  Assembly_Assembly_BLASTn:
+    run: ../task_types/tt_assm_assm_blastn_wnode.cwl
+    in:
+      queries_gc_id_list: Extract_Input_GenColl_IDs/gc_id_list
+      subjects_gc_id_list: Extract_Top_Assemblies/gc_id_list
+      # this will brea here
+      Get_Top_Assemblies_GenColl_ASN_assemblies: Get_Top_Assemblies_GenColl_ASN/gencoll_asn
+      gencoll_asn: gencoll_asn
+      affinity:
+        default: 'subject'
+      # settings
+      asn_cache: asn_cache
+      compart: 
+        default: "true"
+      evalue: 
+        default: 0.0001
+      gapextend: 
+        default: 1
+      gapopen: 
+        default: 2
+      max_bases_per_call: 
+        default: 500000000
+      max_target_seqs: 
+        default: 250
+      merge_align_filter: 
+        default: "((reciprocity = 3 AND align_length_ungap >= 5) OR align_length > 1000) AND pct_identity_gap > 25"
+      merge_engine: 
+        default: "tree-merger"
+      soft_masking:  
+        default: "true"
+      task:  
+        default: megablast
+      use_common_components:  
+        default: "true"
+      window_size:  
+        default: 150
+      word_size:  
+        default: 28
+      workers_per_cpu:  
+        default:  0.4
+    out: [blast_align]
+  Identify_Top_N_ANI:
+    run: ../task_types/tt_ani_top_n.cwl
+    in:
+        asn_cache: asn_cache
+        ANI_cutoff: ANI_cutoff
+        gencoll_asn: gencoll_asn
+        blast_align: Assembly_Assembly_BLASTn/blast_align
+        ref_assembly_taxid: ref_assembly_taxid
+    out: [top,annot]