cwlVersion: v1.2; JIRA: PGAPX-910

ncbi · Apr 7, 2021 · 72804b6 · 72804b6
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commit 72804b6
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Showing 256 changed files with 256 additions and 256 deletions.
diff --git a/assemble.cwl b/assemble.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.2
 doc: |
   Assemble a set of reads using SKESA
 requirements:

diff --git a/bacterial_annot/bacterial_hit_mapping.cwl b/bacterial_annot/bacterial_hit_mapping.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "bacterial_hit_mapping"
 
 class: CommandLineTool

diff --git a/bacterial_annot/get_off_frame_orfs.cwl b/bacterial_annot/get_off_frame_orfs.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Get off-frame ORFs"
 class: CommandLineTool
 

diff --git a/bacterial_annot/gpx_qdump.cwl b/bacterial_annot/gpx_qdump.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Search All HMMs, gather"
 class: CommandLineTool
 

diff --git a/bacterial_annot/wf_bacterial_annot_pass1.cwl b/bacterial_annot/wf_bacterial_annot_pass1.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:

diff --git a/bacterial_annot/wf_bacterial_annot_pass2.cwl b/bacterial_annot/wf_bacterial_annot_pass2.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 requirements:
     - class: SubworkflowFeatureRequirement

diff --git a/bacterial_annot/wf_bacterial_annot_pass3.cwl b/bacterial_annot/wf_bacterial_annot_pass3.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 requirements:
     - class: SubworkflowFeatureRequirement

diff --git a/bacterial_annot/wf_bacterial_annot_pass4.cwl b/bacterial_annot/wf_bacterial_annot_pass4.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 requirements:
     - class: SubworkflowFeatureRequirement

diff --git a/bacterial_kmer/wf_bacterial_kmer.cwl b/bacterial_kmer/wf_bacterial_kmer.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: bacterial_kmer
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow 
 requirements: 
     - class: SubworkflowFeatureRequirement    

diff --git a/bacterial_mobile_elem/gpx_qdump.cwl b/bacterial_mobile_elem/gpx_qdump.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Execute CRISPR, gather"
 class: CommandLineTool
 

diff --git a/bacterial_mobile_elem/gpx_qsubmit.cwl b/bacterial_mobile_elem/gpx_qsubmit.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Execute CRISPR, scatter"
 class: CommandLineTool
 

diff --git a/bacterial_mobile_elem/ncbi_crisper_wnode.cwl b/bacterial_mobile_elem/ncbi_crisper_wnode.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Execute CRISPR, execution"
 class: CommandLineTool
 

diff --git a/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl b/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Execute CRISPR"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 #requirements:

diff --git a/bacterial_ncrna/annot_merge.cwl b/bacterial_ncrna/annot_merge.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Post-process CMsearch annotations"
 class: CommandLineTool
 

diff --git a/bacterial_ncrna/cmsearch_wnode.cwl b/bacterial_ncrna/cmsearch_wnode.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run genomic CMsearch (Rfam rRNA), execution"
 class: CommandLineTool
 

diff --git a/bacterial_ncrna/gpx_qdump.cwl b/bacterial_ncrna/gpx_qdump.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run genomic CMsearch (Rfam rRNA), gather"
 class: CommandLineTool
 

diff --git a/bacterial_ncrna/gpx_qsubmit.cwl b/bacterial_ncrna/gpx_qsubmit.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run genomic CMsearch (Rfam rRNA), scatter"
 class: CommandLineTool
 

diff --git a/bacterial_ncrna/wf_gcmsearch.cwl b/bacterial_ncrna/wf_gcmsearch.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Run genomic CMsearch (Rfam rRNA)"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 #requirements:

diff --git a/bacterial_noncoding/align_merge.cwl b/bacterial_noncoding/align_merge.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Merge rRNA Alignments"
 class: CommandLineTool
 

diff --git a/bacterial_noncoding/annot_merge.cwl b/bacterial_noncoding/annot_merge.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Post-process CMsearch annotations"
 class: CommandLineTool
 

diff --git a/bacterial_noncoding/cmsearch_wnode.cwl b/bacterial_noncoding/cmsearch_wnode.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run genomic CMsearch, execution"
 class: CommandLineTool
 

diff --git a/bacterial_noncoding/gpx_make_outputs.cwl b/bacterial_noncoding/gpx_make_outputs.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "BLAST against rRNA db, gather"
 class: CommandLineTool
 

diff --git a/bacterial_noncoding/gpx_qdump.cwl b/bacterial_noncoding/gpx_qdump.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run genomic CMsearch (5S rRNA), gather"
 class: CommandLineTool
 

diff --git a/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl b/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run genomic CMsearch (5S rRNA), scatter"
 class: CommandLineTool
 

diff --git a/bacterial_noncoding/ribosomal_align2annot.cwl b/bacterial_noncoding/ribosomal_align2annot.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Generate rRNA Annotation"
 class: CommandLineTool
 

diff --git a/bacterial_noncoding/wf_bacterial_noncoding.cwl b/bacterial_noncoding/wf_bacterial_noncoding.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Non-Coding Bacterial Genes"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:

diff --git a/bacterial_noncoding/wf_gcmsearch.cwl b/bacterial_noncoding/wf_gcmsearch.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Run genomic CMsearch"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 #requirements:

diff --git a/bacterial_prepare_unannotated.cwl b/bacterial_prepare_unannotated.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Prepare Unannotated Sequences"
 doc: "Prepare Unannotated Sequences"
 class: CommandLineTool

diff --git a/bacterial_trna/gpx_qdump.cwl b/bacterial_trna/gpx_qdump.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run tRNAScan, gather"
 class: CommandLineTool
 

diff --git a/bacterial_trna/gpx_qsubmit_trnascan.cwl b/bacterial_trna/gpx_qsubmit_trnascan.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run tRNAScan, scatter"
 class: CommandLineTool
 

diff --git a/bacterial_trna/trnascan_dump.cwl b/bacterial_trna/trnascan_dump.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run tRNAScan, transform"
 class: CommandLineTool
 

diff --git a/bacterial_trna/trnascan_wnode.cwl b/bacterial_trna/trnascan_wnode.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Run tRNAScan, execution"
 class: CommandLineTool
 

diff --git a/bacterial_trna/wf_scan_and_dump.cwl b/bacterial_trna/wf_scan_and_dump.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 
 class: Workflow
 

diff --git a/bacterial_trna/wf_trnascan.cwl b/bacterial_trna/wf_trnascan.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Run tRNAScan"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:

diff --git a/cache_entrez_gene.cwl b/cache_entrez_gene.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Cache Entrez Gene"
 class: CommandLineTool
 

diff --git a/clade_assign/align_sort.cwl b/clade_assign/align_sort.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: "Assign Clade, align_sort"

diff --git a/clade_assign/assign_clade_bacteria.cwl b/clade_assign/assign_clade_bacteria.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: "Assign Clade, assign_clade_bacteria"

diff --git a/clade_assign/gpx_make_outputs.cwl b/clade_assign/gpx_make_outputs.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: "Find Marker Alignments, gather"

diff --git a/clade_assign/gpx_qsubmit.cwl b/clade_assign/gpx_qsubmit.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: "Find Marker Alignments, scatter"

diff --git a/clade_assign/tblastn_wnode.cwl b/clade_assign/tblastn_wnode.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: Find Marker Alignments, execute"

diff --git a/clade_assign/wf_assign_clade.cwl b/clade_assign/wf_assign_clade.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 label: "Assign Clade"

diff --git a/clade_assign/wf_clade_assign.cwl b/clade_assign/wf_clade_assign.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 label: "Assign Clade plane complete workflow"

diff --git a/clade_assign/wf_find_marker_alignments.cwl b/clade_assign/wf_find_marker_alignments.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 label: "Find Marker Alignments"

diff --git a/expr/ani.cwl b/expr/ani.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 label: "Split input directory into subpath flows for top level user workflow ani.cwl"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: ExpressionTool
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/expr/blast_hits_cache_data_split_dir.cwl b/expr/blast_hits_cache_data_split_dir.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 label: "Split input directory into subpath flows"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: ExpressionTool
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/expr/supplemental_data_split_dir.cwl b/expr/supplemental_data_split_dir.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 label: "Split input directory into subpath flows"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: ExpressionTool
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/genomic_source/gc_asm_xml_description.cwl b/genomic_source/gc_asm_xml_description.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Extract Assembly Information II"
 class: CommandLineTool
 

diff --git a/genomic_source/gc_create.cwl b/genomic_source/gc_create.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Create Assembly From Sequences"
 class: CommandLineTool
 

diff --git a/genomic_source/gc_get_molecules.cwl b/genomic_source/gc_get_molecules.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Extract Assembly Information I"
 class: CommandLineTool
 

diff --git a/genomic_source/prime_cache.cwl b/genomic_source/prime_cache.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Cache FASTA Sequences"
 class: CommandLineTool
 

diff --git a/genomic_source/wf_genomic_source.cwl b/genomic_source/wf_genomic_source.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Create Genomic Collection for Bacterial Pipeline"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:

diff --git a/genomic_source/wf_genomic_source_asn.cwl b/genomic_source/wf_genomic_source_asn.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 label: "Create Genomic Collection for Bacterial Pipeline, ASN.1 input"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:

diff --git a/pgap.cwl b/pgap.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.2
 doc: |
   PGAP pipeline for external usage, powered via containers,
   simple user input:  (FASTA + yaml only, no template)

diff --git a/prepare_user_input.cwl b/prepare_user_input.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 label: "Prepare user input"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 doc: Prepare user input for  NCBI-PGAP pipeline
 

diff --git a/prepare_user_input2.cwl b/prepare_user_input2.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 label: "Prepare user input"
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 doc: Prepare user input for  NCBI-PGAP pipeline
 

diff --git a/preserve_annot_markup.cwl b/preserve_annot_markup.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 label: "Preserve Product Accessions"
 class: CommandLineTool