From 72804b6506c9f54ec75627f82aafe6a28d7a49fa Mon Sep 17 00:00:00 2001 From: "Badretdin, Azat" Date: Wed, 7 Apr 2021 07:42:22 -0400 Subject: [PATCH] cwlVersion: v1.2; JIRA: PGAPX-910 --- assemble.cwl | 2 +- bacterial_annot/bacterial_hit_mapping.cwl | 2 +- bacterial_annot/get_off_frame_orfs.cwl | 2 +- bacterial_annot/gpx_qdump.cwl | 2 +- bacterial_annot/wf_bacterial_annot_pass1.cwl | 2 +- bacterial_annot/wf_bacterial_annot_pass2.cwl | 2 +- bacterial_annot/wf_bacterial_annot_pass3.cwl | 2 +- bacterial_annot/wf_bacterial_annot_pass4.cwl | 2 +- bacterial_kmer/wf_bacterial_kmer.cwl | 2 +- bacterial_mobile_elem/gpx_qdump.cwl | 2 +- bacterial_mobile_elem/gpx_qsubmit.cwl | 2 +- bacterial_mobile_elem/ncbi_crisper_wnode.cwl | 2 +- bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl | 2 +- bacterial_ncrna/annot_merge.cwl | 2 +- bacterial_ncrna/cmsearch_wnode.cwl | 2 +- bacterial_ncrna/gpx_qdump.cwl | 2 +- bacterial_ncrna/gpx_qsubmit.cwl | 2 +- bacterial_ncrna/wf_gcmsearch.cwl | 2 +- bacterial_noncoding/align_merge.cwl | 2 +- bacterial_noncoding/annot_merge.cwl | 2 +- bacterial_noncoding/cmsearch_wnode.cwl | 2 +- bacterial_noncoding/gpx_make_outputs.cwl | 2 +- bacterial_noncoding/gpx_qdump.cwl | 2 +- bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl | 2 +- bacterial_noncoding/ribosomal_align2annot.cwl | 2 +- bacterial_noncoding/wf_bacterial_noncoding.cwl | 2 +- bacterial_noncoding/wf_gcmsearch.cwl | 2 +- bacterial_prepare_unannotated.cwl | 2 +- bacterial_trna/gpx_qdump.cwl | 2 +- bacterial_trna/gpx_qsubmit_trnascan.cwl | 2 +- bacterial_trna/trnascan_dump.cwl | 2 +- bacterial_trna/trnascan_wnode.cwl | 2 +- bacterial_trna/wf_scan_and_dump.cwl | 2 +- bacterial_trna/wf_trnascan.cwl | 2 +- cache_entrez_gene.cwl | 2 +- clade_assign/align_sort.cwl | 2 +- clade_assign/assign_clade_bacteria.cwl | 2 +- clade_assign/gpx_make_outputs.cwl | 2 +- clade_assign/gpx_qsubmit.cwl | 2 +- clade_assign/tblastn_wnode.cwl | 2 +- clade_assign/wf_assign_clade.cwl | 2 +- clade_assign/wf_clade_assign.cwl | 2 +- clade_assign/wf_find_marker_alignments.cwl | 2 +- expr/ani.cwl | 2 +- expr/blast_hits_cache_data_split_dir.cwl | 2 +- expr/supplemental_data_split_dir.cwl | 2 +- genomic_source/gc_asm_xml_description.cwl | 2 +- genomic_source/gc_create.cwl | 2 +- genomic_source/gc_get_molecules.cwl | 2 +- genomic_source/prime_cache.cwl | 2 +- genomic_source/wf_genomic_source.cwl | 2 +- genomic_source/wf_genomic_source_asn.cwl | 2 +- pgap.cwl | 2 +- prepare_user_input.cwl | 2 +- prepare_user_input2.cwl | 2 +- preserve_annot_markup.cwl | 2 +- progs/add_locus_tags.cwl | 2 +- progs/add_prot_names_to_annot.cwl | 2 +- progs/align_filter.cwl | 2 +- progs/align_find_frequent_sas.cwl | 2 +- progs/align_merge.cwl | 2 +- progs/align_sort.cwl | 2 +- progs/ani_top_identification.cwl | 2 +- progs/annot_checksum.cwl | 2 +- progs/annot_ribo_operons.cwl | 2 +- progs/asn2fasta.cwl | 2 +- progs/asn2flat.cwl | 2 +- progs/asn_cleanup.cwl | 2 +- progs/asn_translator.cwl | 2 +- progs/asndisc_cpp.cwl | 2 +- progs/asnvalidate.cwl | 2 +- progs/assign_cluster.cwl | 2 +- progs/assign_hmm.cwl | 2 +- progs/assm_assm_blastn_create_jobs.cwl | 2 +- progs/assm_assm_blastn_wnode.cwl | 2 +- progs/bact_annot_filter.cwl | 2 +- progs/bact_asn_stats.cwl | 2 +- progs/bact_best_evidence_alignments.cwl | 2 +- progs/bact_entries_merge.cwl | 2 +- progs/bact_filter_preserved.cwl | 2 +- progs/bact_get_kmer_reference.cwl | 2 +- progs/bact_univ_prot_stats.cwl | 2 +- progs/bacterial_resolve_conflicts.cwl | 2 +- progs/blastn_wnode.cwl | 2 +- progs/cache_kmer.cwl | 2 +- progs/cat.cwl | 2 +- progs/catlog.cwl | 2 +- progs/cluster_blastp_wnode.cwl | 2 +- progs/collect_annot_stats.cwl | 2 +- progs/combine_kmer_sqlite.cwl | 2 +- progs/compute_gencode.cwl | 2 +- progs/dumb_down_as_required.cwl | 2 +- progs/ent2sqn.cwl | 2 +- progs/extract_gencoll_ids.cwl | 2 +- progs/famReport.cwl | 2 +- progs/fastaval.cwl | 2 +- progs/file2basenames.cwl | 2 +- progs/file2int.cwl | 2 +- progs/file2ints.cwl | 2 +- progs/file2string.cwl | 2 +- progs/final_bact_asn.cwl | 2 +- progs/format_rrnas.cwl | 2 +- progs/fscr_calls_pass1.cwl | 2 +- progs/fscr_format_calls.cwl | 2 +- progs/gbproject.cwl | 2 +- progs/gc_extract_ids.cwl | 2 +- progs/gc_get_assembly.cwl | 2 +- progs/gc_get_molecules.cwl | 2 +- progs/gencode2trnamodel.cwl | 2 +- progs/genemark.cwl | 2 +- progs/genemark_post.cwl | 2 +- progs/genemark_training.cwl | 2 +- progs/generate_fscr_feats.cwl | 2 +- progs/gp_annot_format.cwl | 2 +- progs/gp_fetch_sequences.cwl | 2 +- progs/gp_getorf.cwl | 2 +- progs/gp_makeblastdb.cwl | 2 +- progs/gpx_make_outputs.cwl | 2 +- progs/gpx_qdump.cwl | 2 +- progs/gpx_qsubmit-xml.cwl | 2 +- progs/gpx_qsubmit.cwl | 2 +- progs/hmmsearch_create_jobs.cwl | 2 +- progs/hmmsearch_wnode.cwl | 2 +- progs/identify_wp.cwl | 2 +- progs/kmer_build_tree.cwl | 2 +- progs/kmer_compare_wnode.cwl | 2 +- progs/kmer_extract_wnode.cwl | 2 +- progs/kmer_files2sqlite.cwl | 2 +- progs/kmer_top_identification.cwl | 2 +- progs/kmer_top_n_extract.cwl | 2 +- progs/lds2_indexer.cwl | 2 +- progs/list_kmer_sqlite.cwl | 2 +- progs/orf_hits_cache_retrieve.cwl | 2 +- progs/pgaap_prepare_review.cwl | 2 +- progs/pgapx_input_check.cwl | 2 +- progs/pgapx_yaml_ctl.cwl | 2 +- progs/pinger.cwl | 2 +- progs/prepare_seq_entry_input.cwl | 2 +- progs/prepare_sparclbl_input.cwl | 2 +- progs/prime_cache.cwl | 2 +- progs/proc_annot_stats.cwl | 2 +- progs/protein_extract.cwl | 2 +- progs/reduce.cwl | 2 +- progs/screen_evaluate.cwl | 2 +- progs/separate_plasmid_orfs.cwl | 2 +- progs/set_operation.cwl | 2 +- progs/skesa.cwl | 2 +- progs/sparclbl.cwl | 2 +- progs/sqn2gbent.cwl | 2 +- progs/std_validation.cwl | 2 +- progs/submit_kmer_compare.cwl | 2 +- progs/submit_kmer_compare_tmp_pairwise.cwl | 2 +- progs/submit_kmer_extract.cwl | 2 +- progs/taxonomy_check_16S.cwl | 2 +- progs/unit_tests/test_add_locus_tags/test.cwl | 2 +- progs/unit_tests/test_asn2fasta/test.cwl | 2 +- progs/unit_tests/test_asn2flat/test.cwl | 2 +- progs/unit_tests/test_asn_cleanup/test.cwl | 2 +- progs/unit_tests/test_bacterial_prot_src/test.cwl | 2 +- progs/unit_tests/test_cluster_blastp_wnode/test.cwl | 2 +- progs/unit_tests/test_collect_annot_stats/test.cwl | 2 +- progs/unit_tests/test_combine_kmer_sqlite/test.cwl | 2 +- progs/unit_tests/test_compute_gencode/test.cwl | 2 +- progs/unit_tests/test_dumb_down_as_required/test.cwl | 2 +- progs/unit_tests/test_ent2sqn/test.cwl | 2 +- progs/unit_tests/test_final_bact_asn/test.cwl | 2 +- progs/unit_tests/test_gencode2trnamodel/test.cwl | 2 +- progs/unit_tests/test_gp_annot_format/test.cwl | 2 +- progs/unit_tests/test_js_extra_spaces/cat.cwl | 2 +- progs/unit_tests/test_js_extra_spaces/test.cwl | 2 +- progs/unit_tests/test_kmer_compare_wnode/test.cwl | 2 +- progs/unit_tests/test_kmer_extract_wnode/test.cwl | 2 +- progs/unit_tests/test_kmer_files2sqlite/test.cwl | 2 +- progs/unit_tests/test_kmer_top_identification/test.cwl | 2 +- progs/unit_tests/test_list_kmer_sqlite/test.cwl | 2 +- progs/unit_tests/test_preserve_annot_markup/test.cwl | 2 +- progs/unit_tests/test_prime_cache/test.cwl | 2 +- progs/unit_tests/test_sparclbl/test.cwl | 2 +- progs/unit_tests/test_sqn2gbent/test.cwl | 2 +- progs/unit_tests/test_std_validation/test.cwl | 2 +- progs/unit_tests/test_trnascan_wnode/test.cwl | 2 +- progs/unit_tests/test_univ_prot_stats/test.cwl | 2 +- progs/unit_tests/test_val_format/test.cwl | 2 +- progs/unit_tests/test_val_format/val_format.cwl | 2 +- progs/unit_tests/test_val_stats/test.cwl | 2 +- progs/unit_tests/test_xml_evaluate/test.cwl | 2 +- progs/unit_tests/test_xsltproc/test.cwl | 2 +- progs/univec_wnode.cwl | 2 +- progs/val_format.cwl | 2 +- progs/val_stats.cwl | 2 +- progs/xml_evaluate.cwl | 2 +- progs/xsltproc.cwl | 2 +- progs/yaml2json.cwl | 2 +- protein_alignment/align_filter.cwl | 2 +- protein_alignment/align_sort.cwl | 2 +- protein_alignment/bacterial_prot_src.cwl | 2 +- protein_alignment/bacterial_protalign_filter.cwl | 2 +- protein_alignment/cat.cwl | 2 +- protein_alignment/cut_job_path.cwl | 2 +- protein_alignment/gpx_make_outputs.cwl | 2 +- protein_alignment/gpx_qdump.cwl | 2 +- protein_alignment/gpx_qdump_pro.cwl | 2 +- protein_alignment/gpx_qsubmit.cwl | 2 +- protein_alignment/gpx_qsubmit_1.cwl | 2 +- protein_alignment/gpx_qsubmit_pro.cwl | 2 +- protein_alignment/prosplign_compart.cwl | 2 +- protein_alignment/prosplign_compart_filter.cwl | 2 +- protein_alignment/prosplign_wnode.cwl | 2 +- protein_alignment/tblastn_wnode.cwl | 2 +- protein_alignment/tblastn_wnode_1.cwl | 2 +- protein_alignment/wf_align_filter.cwl | 2 +- protein_alignment/wf_compart_filter_prosplign.cwl | 2 +- protein_alignment/wf_protein_alignment.cwl | 2 +- protein_alignment/wf_seed.cwl | 2 +- protein_alignment/wf_seed_1.cwl | 2 +- split_jobs/cat_array_of_files.cwl | 2 +- split_jobs/split.cwl | 2 +- spurious_annot/wf_spurious_annot_pass1.cwl | 2 +- spurious_annot/wf_spurious_annot_pass2.cwl | 2 +- task_types/tt_align_filter_sa.cwl | 2 +- task_types/tt_align_merge_sas.cwl | 2 +- task_types/tt_align_sort_sa.cwl | 2 +- task_types/tt_ani_top_n.cwl | 2 +- task_types/tt_assm_assm_blastn_wnode.cwl | 2 +- task_types/tt_bact_get_kmer_reference.cwl | 2 +- task_types/tt_blastn_wnode.cwl | 2 +- task_types/tt_blastp_wnode_naming.cwl | 2 +- task_types/tt_blastp_wnode_struct.cwl | 2 +- task_types/tt_cache_asnb_entries.cwl | 2 +- task_types/tt_cluster_and_qdump.cwl | 2 +- task_types/tt_extract_gencoll_ids.cwl | 2 +- task_types/tt_format_rrnas_from_seq_entry.cwl | 2 +- task_types/tt_fscr_calls_pass1.cwl | 2 +- task_types/tt_gcaccess_from_list.cwl | 2 +- task_types/tt_hmmsearch_wnode.cwl | 2 +- task_types/tt_hmmsearch_wnode_plus_qdump.cwl | 2 +- task_types/tt_kmer_build_tree.cwl | 2 +- task_types/tt_kmer_cache_retrieve.cwl | 2 +- task_types/tt_kmer_cache_store.cwl | 2 +- task_types/tt_kmer_compare_wnode.cwl | 2 +- task_types/tt_kmer_gc_extract_wnode.cwl | 2 +- task_types/tt_kmer_ref_compare_wnode.cwl | 2 +- task_types/tt_kmer_seq_entry_extract_wnode.cwl | 2 +- task_types/tt_kmer_top_n.cwl | 2 +- task_types/tt_kmer_top_n_extract.cwl | 2 +- task_types/tt_preserve_annot.cwl | 2 +- task_types/tt_taxonomy_check_16S.cwl | 2 +- task_types/tt_univec_wnode.cwl | 2 +- taxcheck.cwl | 2 +- taxonomy_check_16S/wf_taxonomy_check_16S.cwl | 2 +- vecscreen/bacterial_screening.cwl | 2 +- vecscreen/foreign_screening.cwl | 2 +- vecscreen/vecscreen.cwl | 2 +- wf_bacterial_prot_src.cwl | 2 +- wf_common.cwl | 2 +- wf_pgap_simple.cwl | 2 +- 256 files changed, 256 insertions(+), 256 deletions(-) diff --git a/assemble.cwl b/assemble.cwl index 65ee88a..12a852f 100755 --- 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 index 0a5cba3..ac02f3a 100644 --- 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 index fee17dc..3c07f85 100644 --- 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 index ef8ea9f..0f462f4 100644 --- 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 index 22f24e9..61aa71c 100755 --- 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 index 817daa1..93e9897 100755 --- 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 index af8384e..0308d1d 100755 --- 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 index 636629a..52c5830 100755 --- 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 index 9ef80ac..3b7b522 100644 --- 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 index 656d704..0fdcc86 100644 --- 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 index 8f86cd3..6104e81 100644 --- 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 index 5abb1e0..d8e53f1 100644 --- 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 index e01ac10..241827b 100755 --- 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 index 1450a0a..82237b9 100644 --- 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 index 9a0f429..003fbc5 100644 --- 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 index e24ed81..6bf6514 100644 --- 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 index da6ecb3..9fd79b0 100644 --- 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 index 2bbf89f..4e6cac4 100755 --- 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 index 049aa64..53718aa 100644 --- 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 index 9e07738..1662287 100644 --- 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 index b7454a0..a637d70 100644 --- 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 index a0b95a0..0e62c77 100644 --- 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 index f303704..0134637 100644 --- 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 index fc93aa0..8f424da 100644 --- 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 index d9dcba2..da5d289 100644 --- 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 index caf63f9..cd4ed7a 100755 --- 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 index c643c0b..7859024 100755 --- 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 index a721574..022571b 100644 --- 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 index 8a18653..4be1389 100644 --- 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 index 94b2471..98b7ada 100644 --- 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 index 2ba8011..c545f06 100644 --- 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 index 9d6d007..8446fe8 100644 --- 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 index b642c54..edb293f 100644 --- 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 index 0ccf109..dce6efc 100755 --- 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 index bb06c8e..3fe65e9 100644 --- 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 index c4ea264..f8edbff 100644 --- 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 index e8c4a54..ee8eaea 100644 --- 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 index 283c24b..f2599d7 100644 --- 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 index 70a814d..69bd13a 100644 --- 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 index a26a03c..2f40c70 100644 --- 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 index b07e7a6..19d6c5a 100644 --- 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 index 6c5bb21..c1295e3 100644 --- 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 index 0806468..5cc801b 100755 --- 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 index 97271dd..b2a1b9a 100644 --- 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 index ee93347..71ccdb5 100644 --- 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 index 8eab0c9..0dd396b 100644 --- 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 index 3a474e6..c8c1902 100644 --- 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 index 27671c5..709f609 100644 --- 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 index ca6ee50..18ea639 100644 --- 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 index 4d90301..b0208b7 100644 --- 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 index c36ec48..c2e74e5 100755 --- 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 index d07cc90..600e292 100755 --- 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 index 2c16bfd..e05d30d 100755 --- 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 index 2323c9c..dd1d6f8 100755 --- 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 index 0dd90cf..5e75e3c 100644 --- 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 index 0a8e89b..e3f68a4 100644 --- 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 diff --git a/progs/add_locus_tags.cwl b/progs/add_locus_tags.cwl index cfee6de..4c48c19 100644 --- a/progs/add_locus_tags.cwl +++ b/progs/add_locus_tags.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "add_locus_tags" class: CommandLineTool diff --git a/progs/add_prot_names_to_annot.cwl b/progs/add_prot_names_to_annot.cwl index 6f55c9f..fb977c2 100644 --- a/progs/add_prot_names_to_annot.cwl +++ b/progs/add_prot_names_to_annot.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "add_prot_names_to_annot" class: CommandLineTool diff --git a/progs/align_filter.cwl b/progs/align_filter.cwl index ee6e7be..75e229b 100644 --- a/progs/align_filter.cwl +++ b/progs/align_filter.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "align_filter" class: CommandLineTool diff --git a/progs/align_find_frequent_sas.cwl b/progs/align_find_frequent_sas.cwl index e3a3d7b..7b47fdd 100644 --- a/progs/align_find_frequent_sas.cwl +++ b/progs/align_find_frequent_sas.cwl @@ -3,7 +3,7 @@ $namespaces: id: align_find_frequent label: align_find_frequent_sas class: CommandLineTool -cwlVersion: v1.0 +cwlVersion: v1.2 baseCommand: align_find_frequent doc: '' inputs: diff --git a/progs/align_merge.cwl b/progs/align_merge.cwl index 722e215..4c4361d 100644 --- a/progs/align_merge.cwl +++ b/progs/align_merge.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "align_merge" class: CommandLineTool diff --git a/progs/align_sort.cwl b/progs/align_sort.cwl index 08853a4..bad04ee 100644 --- a/progs/align_sort.cwl +++ b/progs/align_sort.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "align_sort" class: CommandLineTool diff --git a/progs/ani_top_identification.cwl b/progs/ani_top_identification.cwl index d28e33e..bada9a4 100644 --- a/progs/ani_top_identification.cwl +++ b/progs/ani_top_identification.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "ani_top_identification" # file: progs/ani_top_identification.cwl diff --git a/progs/annot_checksum.cwl b/progs/annot_checksum.cwl index 48b9ece..374e2c2 100644 --- a/progs/annot_checksum.cwl +++ b/progs/annot_checksum.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner class: CommandLineTool baseCommand: annot_checksum -cwlVersion: v1.0 +cwlVersion: v1.2 inputs: input: type: File? diff --git a/progs/annot_ribo_operons.cwl b/progs/annot_ribo_operons.cwl index d7298b0..a2f620a 100644 --- a/progs/annot_ribo_operons.cwl +++ b/progs/annot_ribo_operons.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: annot_ribo_operons label: annot_ribo_operons diff --git a/progs/asn2fasta.cwl b/progs/asn2fasta.cwl index a595800..9702ac2 100644 --- a/progs/asn2fasta.cwl +++ b/progs/asn2fasta.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asn2fasta" class: CommandLineTool diff --git a/progs/asn2flat.cwl b/progs/asn2flat.cwl index 56cd293..6ce05c5 100644 --- a/progs/asn2flat.cwl +++ b/progs/asn2flat.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asn2flat" class: CommandLineTool diff --git a/progs/asn_cleanup.cwl b/progs/asn_cleanup.cwl index f3f78ad..c0dc63d 100644 --- a/progs/asn_cleanup.cwl +++ b/progs/asn_cleanup.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asn_cleanup" class: CommandLineTool diff --git a/progs/asn_translator.cwl b/progs/asn_translator.cwl index 73167e1..ce5b9b2 100644 --- a/progs/asn_translator.cwl +++ b/progs/asn_translator.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: asn_translator class: CommandLineTool baseCommand: asn_translator diff --git a/progs/asndisc_cpp.cwl b/progs/asndisc_cpp.cwl index 7dd33f2..45a50b2 100644 --- a/progs/asndisc_cpp.cwl +++ b/progs/asndisc_cpp.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asndisc_cpp" class: CommandLineTool diff --git a/progs/asnvalidate.cwl b/progs/asnvalidate.cwl index 4dd93d3..bc80690 100644 --- a/progs/asnvalidate.cwl +++ b/progs/asnvalidate.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asnvalidate" class: CommandLineTool diff --git a/progs/assign_cluster.cwl b/progs/assign_cluster.cwl index 13de2af..ca1a8ac 100644 --- a/progs/assign_cluster.cwl +++ b/progs/assign_cluster.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "assign_cluster" class: CommandLineTool diff --git a/progs/assign_hmm.cwl b/progs/assign_hmm.cwl index b2a9e5f..855bf26 100644 --- a/progs/assign_hmm.cwl +++ b/progs/assign_hmm.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "assign_hmm" class: CommandLineTool diff --git a/progs/assm_assm_blastn_create_jobs.cwl b/progs/assm_assm_blastn_create_jobs.cwl index 9422f6c..4efd2b7 100644 --- a/progs/assm_assm_blastn_create_jobs.cwl +++ b/progs/assm_assm_blastn_create_jobs.cwl @@ -2,7 +2,7 @@ label: "assm_assm_blastn_create_jobs" class: CommandLineTool baseCommand: assm_assm_blastn_create_jobs -cwlVersion: v1.0 +cwlVersion: v1.2 requirements: - class: InlineJavascriptRequirement - class: InitialWorkDirRequirement diff --git a/progs/assm_assm_blastn_wnode.cwl b/progs/assm_assm_blastn_wnode.cwl index 443cf3d..3d147a2 100644 --- a/progs/assm_assm_blastn_wnode.cwl +++ b/progs/assm_assm_blastn_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "assm_assm_blastn_wnode" class: CommandLineTool diff --git a/progs/bact_annot_filter.cwl b/progs/bact_annot_filter.cwl index 8dd635a..ebe52c0 100644 --- a/progs/bact_annot_filter.cwl +++ b/progs/bact_annot_filter.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_annot_filter" class: CommandLineTool diff --git a/progs/bact_asn_stats.cwl b/progs/bact_asn_stats.cwl index 67b3392..e4dcf7b 100644 --- a/progs/bact_asn_stats.cwl +++ b/progs/bact_asn_stats.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_asn_stats" class: CommandLineTool diff --git a/progs/bact_best_evidence_alignments.cwl b/progs/bact_best_evidence_alignments.cwl index 28265a3..88fc114 100644 --- a/progs/bact_best_evidence_alignments.cwl +++ b/progs/bact_best_evidence_alignments.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_best_evidence_alignments" class: CommandLineTool diff --git a/progs/bact_entries_merge.cwl b/progs/bact_entries_merge.cwl index 092b922..43f5715 100644 --- a/progs/bact_entries_merge.cwl +++ b/progs/bact_entries_merge.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_entries_merge" class: CommandLineTool baseCommand: bact_entries_merge diff --git a/progs/bact_filter_preserved.cwl b/progs/bact_filter_preserved.cwl index 9fb014f..b54366b 100644 --- a/progs/bact_filter_preserved.cwl +++ b/progs/bact_filter_preserved.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_filter_preserved" class: CommandLineTool diff --git a/progs/bact_get_kmer_reference.cwl b/progs/bact_get_kmer_reference.cwl index 8055e0a..7528a58 100644 --- a/progs/bact_get_kmer_reference.cwl +++ b/progs/bact_get_kmer_reference.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_get_kmer_reference" class: CommandLineTool diff --git a/progs/bact_univ_prot_stats.cwl b/progs/bact_univ_prot_stats.cwl index db32a11..3a9f031 100644 --- a/progs/bact_univ_prot_stats.cwl +++ b/progs/bact_univ_prot_stats.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_univ_prot_stats" class: CommandLineTool diff --git a/progs/bacterial_resolve_conflicts.cwl b/progs/bacterial_resolve_conflicts.cwl index 5e3bd08..8ff54a3 100644 --- a/progs/bacterial_resolve_conflicts.cwl +++ b/progs/bacterial_resolve_conflicts.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bacterial_resolve_conflicts" class: CommandLineTool diff --git a/progs/blastn_wnode.cwl b/progs/blastn_wnode.cwl index 9ab84a3..aeaed38 100644 --- a/progs/blastn_wnode.cwl +++ b/progs/blastn_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "blastn_wnode" class: CommandLineTool diff --git a/progs/cache_kmer.cwl b/progs/cache_kmer.cwl index b94162a..d80bf04 100644 --- a/progs/cache_kmer.cwl +++ b/progs/cache_kmer.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "cache_kmer" # file: progs/cache_kmer.cwl diff --git a/progs/cat.cwl b/progs/cat.cwl index b79bc4f..885b232 100644 --- a/progs/cat.cwl +++ b/progs/cat.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 baseCommand: cat class: CommandLineTool doc: concatenates input File[] to output File diff --git a/progs/catlog.cwl b/progs/catlog.cwl index 8e9b236..8bdb03c 100644 --- a/progs/catlog.cwl +++ b/progs/catlog.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 baseCommand: cat class: CommandLineTool doc: concatenates input File[] to screen diff --git a/progs/cluster_blastp_wnode.cwl b/progs/cluster_blastp_wnode.cwl index 8a02209..9c66141 100644 --- a/progs/cluster_blastp_wnode.cwl +++ b/progs/cluster_blastp_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "cluster_blastp_wnode" class: CommandLineTool diff --git a/progs/collect_annot_stats.cwl b/progs/collect_annot_stats.cwl index 39ba3c0..7e263d6 100644 --- a/progs/collect_annot_stats.cwl +++ b/progs/collect_annot_stats.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "collect_annot_stats" class: CommandLineTool diff --git a/progs/combine_kmer_sqlite.cwl b/progs/combine_kmer_sqlite.cwl index 3251a68..10c0ffc 100644 --- a/progs/combine_kmer_sqlite.cwl +++ b/progs/combine_kmer_sqlite.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner4 label: combine_kmer_sqlite.cwl doc: Combine together reference kmer store and newly created kmer store for a new assembly -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: combine_kmer_sqlite inputs: diff --git a/progs/compute_gencode.cwl b/progs/compute_gencode.cwl index 53cb3bf..f4c0149 100644 --- a/progs/compute_gencode.cwl +++ b/progs/compute_gencode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "compute_gencode" class: CommandLineTool diff --git a/progs/dumb_down_as_required.cwl b/progs/dumb_down_as_required.cwl index 504adb7..bdb31b0 100644 --- a/progs/dumb_down_as_required.cwl +++ b/progs/dumb_down_as_required.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "dumb_down_as_required" class: CommandLineTool diff --git a/progs/ent2sqn.cwl b/progs/ent2sqn.cwl index 8646485..8658c68 100644 --- a/progs/ent2sqn.cwl +++ b/progs/ent2sqn.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "ent2sqn" class: CommandLineTool diff --git a/progs/extract_gencoll_ids.cwl b/progs/extract_gencoll_ids.cwl index 6779f17..4bad395 100644 --- a/progs/extract_gencoll_ids.cwl +++ b/progs/extract_gencoll_ids.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "extract_gencoll_ids" # File: progs/extract_gencoll_ids.cwl diff --git a/progs/famReport.cwl b/progs/famReport.cwl index b824607..7a65208 100644 --- a/progs/famReport.cwl +++ b/progs/famReport.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "famReport" class: CommandLineTool diff --git a/progs/fastaval.cwl b/progs/fastaval.cwl index fc5e107..6c94bbc 100644 --- a/progs/fastaval.cwl +++ b/progs/fastaval.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: fastaval.sh label: fastaval diff --git a/progs/file2basenames.cwl b/progs/file2basenames.cwl index 4849510..cf25380 100644 --- a/progs/file2basenames.cwl +++ b/progs/file2basenames.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: ExpressionTool requirements: { InlineJavascriptRequirement: {} } diff --git a/progs/file2int.cwl b/progs/file2int.cwl index 6866db2..fc26d61 100644 --- a/progs/file2int.cwl +++ b/progs/file2int.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: ExpressionTool requirements: { InlineJavascriptRequirement: {} } diff --git a/progs/file2ints.cwl b/progs/file2ints.cwl index 87922fa..9e36acb 100644 --- a/progs/file2ints.cwl +++ b/progs/file2ints.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: ExpressionTool requirements: { InlineJavascriptRequirement: {} } diff --git a/progs/file2string.cwl b/progs/file2string.cwl index 1a3221a..3f1c7b5 100644 --- a/progs/file2string.cwl +++ b/progs/file2string.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: ExpressionTool requirements: { InlineJavascriptRequirement: {} } diff --git a/progs/final_bact_asn.cwl b/progs/final_bact_asn.cwl index 6db381d..ab6a828 100644 --- a/progs/final_bact_asn.cwl +++ b/progs/final_bact_asn.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "final_bact_asn" class: CommandLineTool diff --git a/progs/format_rrnas.cwl b/progs/format_rrnas.cwl index e9b6c53..daf6706 100644 --- a/progs/format_rrnas.cwl +++ b/progs/format_rrnas.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "format_rrnas" class: CommandLineTool diff --git a/progs/fscr_calls_pass1.cwl b/progs/fscr_calls_pass1.cwl index 75958b1..f90a729 100644 --- a/progs/fscr_calls_pass1.cwl +++ b/progs/fscr_calls_pass1.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: fscr_calls_pass1 label: fscr_calls_pass1 diff --git a/progs/fscr_format_calls.cwl b/progs/fscr_format_calls.cwl index 9f4824c..cc06261 100644 --- a/progs/fscr_format_calls.cwl +++ b/progs/fscr_format_calls.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: fscr_format_calls arguments: [ -nogenbank, -no-taxon-access ] diff --git a/progs/gbproject.cwl b/progs/gbproject.cwl index 4b7f6ec..14e1d1e 100644 --- a/progs/gbproject.cwl +++ b/progs/gbproject.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gbproject" class: CommandLineTool diff --git a/progs/gc_extract_ids.cwl b/progs/gc_extract_ids.cwl index bb06216..98ae143 100644 --- a/progs/gc_extract_ids.cwl +++ b/progs/gc_extract_ids.cwl @@ -2,7 +2,7 @@ label: "gc_extract_ids" class: CommandLineTool baseCommand: gc_extract_ids -cwlVersion: v1.0 +cwlVersion: v1.2 inputs: input: type: File diff --git a/progs/gc_get_assembly.cwl b/progs/gc_get_assembly.cwl index 97b1d80..1ff0d38 100644 --- a/progs/gc_get_assembly.cwl +++ b/progs/gc_get_assembly.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gc_get_assembly" class: CommandLineTool diff --git a/progs/gc_get_molecules.cwl b/progs/gc_get_molecules.cwl index 1c97a96..8eaa0fe 100644 --- a/progs/gc_get_molecules.cwl +++ b/progs/gc_get_molecules.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gc_get_molecules" class: CommandLineTool diff --git a/progs/gencode2trnamodel.cwl b/progs/gencode2trnamodel.cwl index b50597c..b6eaa90 100644 --- a/progs/gencode2trnamodel.cwl +++ b/progs/gencode2trnamodel.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: ExpressionTool requirements: { InlineJavascriptRequirement: {} } diff --git a/progs/genemark.cwl b/progs/genemark.cwl index fa65e18..c03347f 100644 --- a/progs/genemark.cwl +++ b/progs/genemark.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "genemark" class: CommandLineTool diff --git a/progs/genemark_post.cwl b/progs/genemark_post.cwl index ff64525..10a70d7 100644 --- a/progs/genemark_post.cwl +++ b/progs/genemark_post.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "genemark_post" class: CommandLineTool diff --git a/progs/genemark_training.cwl b/progs/genemark_training.cwl index d030a75..b101685 100644 --- a/progs/genemark_training.cwl +++ b/progs/genemark_training.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "genemark_training" class: CommandLineTool diff --git a/progs/generate_fscr_feats.cwl b/progs/generate_fscr_feats.cwl index 3a0cb68..17f1e3d 100644 --- a/progs/generate_fscr_feats.cwl +++ b/progs/generate_fscr_feats.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0 +cwlVersion: v1.2 $namespaces: sbg: 'https://www.sevenbridges.com/' id: generate_fscr_feats diff --git a/progs/gp_annot_format.cwl b/progs/gp_annot_format.cwl index 8a29630..786476d 100644 --- a/progs/gp_annot_format.cwl +++ b/progs/gp_annot_format.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gp_annot_format" class: CommandLineTool diff --git a/progs/gp_fetch_sequences.cwl b/progs/gp_fetch_sequences.cwl index 5c03dba..402feae 100644 --- a/progs/gp_fetch_sequences.cwl +++ b/progs/gp_fetch_sequences.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gp_fetch_sequences" class: CommandLineTool diff --git a/progs/gp_getorf.cwl b/progs/gp_getorf.cwl index 6db9f1d..d0ad762 100644 --- a/progs/gp_getorf.cwl +++ b/progs/gp_getorf.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gp_getorf" class: CommandLineTool diff --git a/progs/gp_makeblastdb.cwl b/progs/gp_makeblastdb.cwl index e9057cb..b6039a8 100644 --- a/progs/gp_makeblastdb.cwl +++ b/progs/gp_makeblastdb.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gp_makeblastdb" class: Workflow diff --git a/progs/gpx_make_outputs.cwl b/progs/gpx_make_outputs.cwl index 916d1bb..4dc0d28 100644 --- a/progs/gpx_make_outputs.cwl +++ b/progs/gpx_make_outputs.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gpx_make_outputs" class: CommandLineTool diff --git a/progs/gpx_qdump.cwl b/progs/gpx_qdump.cwl index 1908348..b440614 100644 --- a/progs/gpx_qdump.cwl +++ b/progs/gpx_qdump.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gpx_qdump" class: CommandLineTool diff --git a/progs/gpx_qsubmit-xml.cwl b/progs/gpx_qsubmit-xml.cwl index 1c1c898..ca0335e 100644 --- a/progs/gpx_qsubmit-xml.cwl +++ b/progs/gpx_qsubmit-xml.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gpx_qsubmit" doc: > This workflow is specialized for the case when there is an XML input diff --git a/progs/gpx_qsubmit.cwl b/progs/gpx_qsubmit.cwl index 668316b..f839891 100644 --- a/progs/gpx_qsubmit.cwl +++ b/progs/gpx_qsubmit.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gpx_qsubmit" doc: > This workflow is specialized for the case when there is an LDS2 input diff --git a/progs/hmmsearch_create_jobs.cwl b/progs/hmmsearch_create_jobs.cwl index d6af4e8..cef9d3f 100644 --- a/progs/hmmsearch_create_jobs.cwl +++ b/progs/hmmsearch_create_jobs.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "hmmsearch_create_jobs" class: CommandLineTool diff --git a/progs/hmmsearch_wnode.cwl b/progs/hmmsearch_wnode.cwl index 3086cdf..281b5ce 100644 --- a/progs/hmmsearch_wnode.cwl +++ b/progs/hmmsearch_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "hmmsearch_wnode" class: CommandLineTool diff --git a/progs/identify_wp.cwl b/progs/identify_wp.cwl index db7409d..85ae05a 100644 --- a/progs/identify_wp.cwl +++ b/progs/identify_wp.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "identify_wp" class: CommandLineTool diff --git a/progs/kmer_build_tree.cwl b/progs/kmer_build_tree.cwl index 764c91e..bfae21b 100644 --- a/progs/kmer_build_tree.cwl +++ b/progs/kmer_build_tree.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_build_tree" class: CommandLineTool diff --git a/progs/kmer_compare_wnode.cwl b/progs/kmer_compare_wnode.cwl index 0cc0a9d..1af6382 100644 --- a/progs/kmer_compare_wnode.cwl +++ b/progs/kmer_compare_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_compare_wnode" class: CommandLineTool diff --git a/progs/kmer_extract_wnode.cwl b/progs/kmer_extract_wnode.cwl index d6b8c9d..8f2aaff 100644 --- a/progs/kmer_extract_wnode.cwl +++ b/progs/kmer_extract_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_extract_wnode" class: CommandLineTool diff --git a/progs/kmer_files2sqlite.cwl b/progs/kmer_files2sqlite.cwl index a05bcb3..9b29775 100644 --- a/progs/kmer_files2sqlite.cwl +++ b/progs/kmer_files2sqlite.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner4 label: kmer_files2sqlite.cwl -cwlVersion: v1.0 +cwlVersion: v1.2 doc: | Convert input .kmer.gz (kmer_file) and .xml (kmer_metadata_file) into new sqlite database diff --git a/progs/kmer_top_identification.cwl b/progs/kmer_top_identification.cwl index c65fb5a..ea1220d 100644 --- a/progs/kmer_top_identification.cwl +++ b/progs/kmer_top_identification.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_top_identification" class: CommandLineTool baseCommand: kmer_top_identification diff --git a/progs/kmer_top_n_extract.cwl b/progs/kmer_top_n_extract.cwl index 983a5df..c4485c1 100644 --- a/progs/kmer_top_n_extract.cwl +++ b/progs/kmer_top_n_extract.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_top_n_extract" class: CommandLineTool diff --git a/progs/lds2_indexer.cwl b/progs/lds2_indexer.cwl index 9dca766..91bfae4 100644 --- a/progs/lds2_indexer.cwl +++ b/progs/lds2_indexer.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "lds2_indexer" class: CommandLineTool diff --git a/progs/list_kmer_sqlite.cwl b/progs/list_kmer_sqlite.cwl index 7626aec..e85762c 100644 --- a/progs/list_kmer_sqlite.cwl +++ b/progs/list_kmer_sqlite.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner doc: Produces the list of all keys in sqlite database -cwlVersion: v1.0 +cwlVersion: v1.2 label: list_kmer_sqlite.cwl baseCommand: list_kmer_sqlite class: CommandLineTool diff --git a/progs/orf_hits_cache_retrieve.cwl b/progs/orf_hits_cache_retrieve.cwl index f19c828..8f1a9dc 100755 --- a/progs/orf_hits_cache_retrieve.cwl +++ b/progs/orf_hits_cache_retrieve.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: orf_hits_cache_retrieve class: CommandLineTool baseCommand: orf_hits_cache_retrieve diff --git a/progs/pgaap_prepare_review.cwl b/progs/pgaap_prepare_review.cwl index c170f40..3bb1ef6 100644 --- a/progs/pgaap_prepare_review.cwl +++ b/progs/pgaap_prepare_review.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "pgaap_prepare_review" class: CommandLineTool diff --git a/progs/pgapx_input_check.cwl b/progs/pgapx_input_check.cwl index ba4e335..65f1b97 100644 --- a/progs/pgapx_input_check.cwl +++ b/progs/pgapx_input_check.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: pgapx_input_check class: CommandLineTool baseCommand: pgapx_input_check diff --git a/progs/pgapx_yaml_ctl.cwl b/progs/pgapx_yaml_ctl.cwl index c6e74ce..478fe47 100644 --- a/progs/pgapx_yaml_ctl.cwl +++ b/progs/pgapx_yaml_ctl.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "pgapx_yaml_ctl" doc: "Converts input JSON file to ASN.1 template" class: CommandLineTool diff --git a/progs/pinger.cwl b/progs/pinger.cwl index 9e0fa10..2f90a32 100644 --- a/progs/pinger.cwl +++ b/progs/pinger.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "pinger" class: CommandLineTool baseCommand: pinger.sh diff --git a/progs/prepare_seq_entry_input.cwl b/progs/prepare_seq_entry_input.cwl index 380e5a5..6ebb483 100644 --- a/progs/prepare_seq_entry_input.cwl +++ b/progs/prepare_seq_entry_input.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "prepare_seq_entry_input" doc: "" class: CommandLineTool diff --git a/progs/prepare_sparclbl_input.cwl b/progs/prepare_sparclbl_input.cwl index 9281336..4887952 100644 --- a/progs/prepare_sparclbl_input.cwl +++ b/progs/prepare_sparclbl_input.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "prepare_sparclbl_input" class: CommandLineTool diff --git a/progs/prime_cache.cwl b/progs/prime_cache.cwl index 38d4226..3462b01 100644 --- a/progs/prime_cache.cwl +++ b/progs/prime_cache.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "prime_cache" class: CommandLineTool diff --git a/progs/proc_annot_stats.cwl b/progs/proc_annot_stats.cwl index df474b7..5040c59 100644 --- a/progs/proc_annot_stats.cwl +++ b/progs/proc_annot_stats.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "proc_annot_stats" class: CommandLineTool diff --git a/progs/protein_extract.cwl b/progs/protein_extract.cwl index aa425b4..da2e6cf 100644 --- a/progs/protein_extract.cwl +++ b/progs/protein_extract.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "protein_extract" class: Workflow diff --git a/progs/reduce.cwl b/progs/reduce.cwl index 6421088..f9a70c0 100644 --- a/progs/reduce.cwl +++ b/progs/reduce.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "reduce" class: CommandLineTool diff --git a/progs/screen_evaluate.cwl b/progs/screen_evaluate.cwl index 3d98234..284db8d 100644 --- a/progs/screen_evaluate.cwl +++ b/progs/screen_evaluate.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: screen_evaluate label: screen_evaluate diff --git a/progs/separate_plasmid_orfs.cwl b/progs/separate_plasmid_orfs.cwl index ae55c3b..31cfa9b 100644 --- a/progs/separate_plasmid_orfs.cwl +++ b/progs/separate_plasmid_orfs.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "separate_plasmid_orfs" class: CommandLineTool baseCommand: separate_plasmid_orfs diff --git a/progs/set_operation.cwl b/progs/set_operation.cwl index 8066cc8..0311a9a 100644 --- a/progs/set_operation.cwl +++ b/progs/set_operation.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "set_operation" class: CommandLineTool diff --git a/progs/skesa.cwl b/progs/skesa.cwl index 33a75e7..898a048 100644 --- a/progs/skesa.cwl +++ b/progs/skesa.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: skesa inputs: diff --git a/progs/sparclbl.cwl b/progs/sparclbl.cwl index fd937c0..42f1985 100644 --- a/progs/sparclbl.cwl +++ b/progs/sparclbl.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "sparclbl" class: CommandLineTool diff --git a/progs/sqn2gbent.cwl b/progs/sqn2gbent.cwl index 9e9475d..2dec7d5 100644 --- a/progs/sqn2gbent.cwl +++ b/progs/sqn2gbent.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "sqn2gbent" class: CommandLineTool diff --git a/progs/std_validation.cwl b/progs/std_validation.cwl index b756837..f3322f6 100644 --- a/progs/std_validation.cwl +++ b/progs/std_validation.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "std_validation" class: CommandLineTool diff --git a/progs/submit_kmer_compare.cwl b/progs/submit_kmer_compare.cwl index 9a29e2e..5f9f31e 100644 --- a/progs/submit_kmer_compare.cwl +++ b/progs/submit_kmer_compare.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "submit_kmer_compare" class: CommandLineTool diff --git a/progs/submit_kmer_compare_tmp_pairwise.cwl b/progs/submit_kmer_compare_tmp_pairwise.cwl index d4940fc..e1073da 100644 --- a/progs/submit_kmer_compare_tmp_pairwise.cwl +++ b/progs/submit_kmer_compare_tmp_pairwise.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "submit_kmer_compare" class: CommandLineTool diff --git a/progs/submit_kmer_extract.cwl b/progs/submit_kmer_extract.cwl index 86a7537..3f3be86 100644 --- a/progs/submit_kmer_extract.cwl +++ b/progs/submit_kmer_extract.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "submit_kmer_extract" doc: > We need $(inputs.seq_entry) to be a local file to the current subdirectory since the file name goes to diff --git a/progs/taxonomy_check_16S.cwl b/progs/taxonomy_check_16S.cwl index 0651a79..d8e9a33 100644 --- a/progs/taxonomy_check_16S.cwl +++ b/progs/taxonomy_check_16S.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "taxonomy_check_16S" class: CommandLineTool diff --git a/progs/unit_tests/test_add_locus_tags/test.cwl b/progs/unit_tests/test_add_locus_tags/test.cwl index aca18b2..3f5d3b8 100755 --- a/progs/unit_tests/test_add_locus_tags/test.cwl +++ b/progs/unit_tests/test_add_locus_tags/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow diff --git a/progs/unit_tests/test_asn2fasta/test.cwl b/progs/unit_tests/test_asn2fasta/test.cwl index 6b91b12..a82229a 100644 --- a/progs/unit_tests/test_asn2fasta/test.cwl +++ b/progs/unit_tests/test_asn2fasta/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asn2fasta" class: Workflow diff --git a/progs/unit_tests/test_asn2flat/test.cwl b/progs/unit_tests/test_asn2flat/test.cwl index 9550eb3..d372593 100644 --- a/progs/unit_tests/test_asn2flat/test.cwl +++ b/progs/unit_tests/test_asn2flat/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asn2flat" class: Workflow diff --git a/progs/unit_tests/test_asn_cleanup/test.cwl b/progs/unit_tests/test_asn_cleanup/test.cwl index 0a5b052..aaaf1cc 100644 --- a/progs/unit_tests/test_asn_cleanup/test.cwl +++ b/progs/unit_tests/test_asn_cleanup/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "asn_cleanup" class: Workflow diff --git a/progs/unit_tests/test_bacterial_prot_src/test.cwl b/progs/unit_tests/test_bacterial_prot_src/test.cwl index c8d3966..91feb85 100644 --- a/progs/unit_tests/test_bacterial_prot_src/test.cwl +++ b/progs/unit_tests/test_bacterial_prot_src/test.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "test bacterial_prot_src" requirements: diff --git a/progs/unit_tests/test_cluster_blastp_wnode/test.cwl b/progs/unit_tests/test_cluster_blastp_wnode/test.cwl index 6f0a21b..6f6a922 100644 --- a/progs/unit_tests/test_cluster_blastp_wnode/test.cwl +++ b/progs/unit_tests/test_cluster_blastp_wnode/test.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "test cluster_blastp_wnode" requirements: diff --git a/progs/unit_tests/test_collect_annot_stats/test.cwl b/progs/unit_tests/test_collect_annot_stats/test.cwl index f6b583e..2dfc166 100755 --- a/progs/unit_tests/test_collect_annot_stats/test.cwl +++ b/progs/unit_tests/test_collect_annot_stats/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_combine_kmer_sqlite/test.cwl b/progs/unit_tests/test_combine_kmer_sqlite/test.cwl index 261ccec..5f5aec0 100644 --- a/progs/unit_tests/test_combine_kmer_sqlite/test.cwl +++ b/progs/unit_tests/test_combine_kmer_sqlite/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "combine_kmer_sqlite" inputs: diff --git a/progs/unit_tests/test_compute_gencode/test.cwl b/progs/unit_tests/test_compute_gencode/test.cwl index ab29579..673ef8e 100644 --- a/progs/unit_tests/test_compute_gencode/test.cwl +++ b/progs/unit_tests/test_compute_gencode/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "compute_gencode" class: Workflow diff --git a/progs/unit_tests/test_dumb_down_as_required/test.cwl b/progs/unit_tests/test_dumb_down_as_required/test.cwl index d29a58a..8ec49e5 100755 --- a/progs/unit_tests/test_dumb_down_as_required/test.cwl +++ b/progs/unit_tests/test_dumb_down_as_required/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_ent2sqn/test.cwl b/progs/unit_tests/test_ent2sqn/test.cwl index 47090ee..353c3b8 100755 --- a/progs/unit_tests/test_ent2sqn/test.cwl +++ b/progs/unit_tests/test_ent2sqn/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: diff --git a/progs/unit_tests/test_final_bact_asn/test.cwl b/progs/unit_tests/test_final_bact_asn/test.cwl index af5c9e0..239608e 100755 --- a/progs/unit_tests/test_final_bact_asn/test.cwl +++ b/progs/unit_tests/test_final_bact_asn/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_gencode2trnamodel/test.cwl b/progs/unit_tests/test_gencode2trnamodel/test.cwl index 84d5536..0c6b866 100644 --- a/progs/unit_tests/test_gencode2trnamodel/test.cwl +++ b/progs/unit_tests/test_gencode2trnamodel/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gencode2trnamodel" class: Workflow diff --git a/progs/unit_tests/test_gp_annot_format/test.cwl b/progs/unit_tests/test_gp_annot_format/test.cwl index f569d62..92b6849 100644 --- a/progs/unit_tests/test_gp_annot_format/test.cwl +++ b/progs/unit_tests/test_gp_annot_format/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gp_annot_format" class: Workflow diff --git a/progs/unit_tests/test_js_extra_spaces/cat.cwl b/progs/unit_tests/test_js_extra_spaces/cat.cwl index 2109a36..36295bb 100644 --- a/progs/unit_tests/test_js_extra_spaces/cat.cwl +++ b/progs/unit_tests/test_js_extra_spaces/cat.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "test 8 space problem" baseCommand: cat diff --git a/progs/unit_tests/test_js_extra_spaces/test.cwl b/progs/unit_tests/test_js_extra_spaces/test.cwl index 8e3473e..4f27ad7 100644 --- a/progs/unit_tests/test_js_extra_spaces/test.cwl +++ b/progs/unit_tests/test_js_extra_spaces/test.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "test 8 space problem" requirements: diff --git a/progs/unit_tests/test_kmer_compare_wnode/test.cwl b/progs/unit_tests/test_kmer_compare_wnode/test.cwl index 9610223..f572e09 100644 --- a/progs/unit_tests/test_kmer_compare_wnode/test.cwl +++ b/progs/unit_tests/test_kmer_compare_wnode/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_compare_wnode" inputs: diff --git a/progs/unit_tests/test_kmer_extract_wnode/test.cwl b/progs/unit_tests/test_kmer_extract_wnode/test.cwl index 1cacbe7..226f528 100644 --- a/progs/unit_tests/test_kmer_extract_wnode/test.cwl +++ b/progs/unit_tests/test_kmer_extract_wnode/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_extract_wnode" class: Workflow diff --git a/progs/unit_tests/test_kmer_files2sqlite/test.cwl b/progs/unit_tests/test_kmer_files2sqlite/test.cwl index 8b98a3b..9bbf835 100644 --- a/progs/unit_tests/test_kmer_files2sqlite/test.cwl +++ b/progs/unit_tests/test_kmer_files2sqlite/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_files2sqlite" inputs: diff --git a/progs/unit_tests/test_kmer_top_identification/test.cwl b/progs/unit_tests/test_kmer_top_identification/test.cwl index 9b490eb..8fef335 100644 --- a/progs/unit_tests/test_kmer_top_identification/test.cwl +++ b/progs/unit_tests/test_kmer_top_identification/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_top_identification.cwl" class: Workflow inputs: diff --git a/progs/unit_tests/test_list_kmer_sqlite/test.cwl b/progs/unit_tests/test_list_kmer_sqlite/test.cwl index 82ae340..cf695c3 100644 --- a/progs/unit_tests/test_list_kmer_sqlite/test.cwl +++ b/progs/unit_tests/test_list_kmer_sqlite/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "list_kmer_sqlite" inputs: diff --git a/progs/unit_tests/test_preserve_annot_markup/test.cwl b/progs/unit_tests/test_preserve_annot_markup/test.cwl index 9d0adee..33a3898 100755 --- a/progs/unit_tests/test_preserve_annot_markup/test.cwl +++ b/progs/unit_tests/test_preserve_annot_markup/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_prime_cache/test.cwl b/progs/unit_tests/test_prime_cache/test.cwl index d8fccae..e87ef3b 100755 --- a/progs/unit_tests/test_prime_cache/test.cwl +++ b/progs/unit_tests/test_prime_cache/test.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/progs/unit_tests/test_sparclbl/test.cwl b/progs/unit_tests/test_sparclbl/test.cwl index 5592775..449a0f9 100755 --- a/progs/unit_tests/test_sparclbl/test.cwl +++ b/progs/unit_tests/test_sparclbl/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "Test sparclbl" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_sqn2gbent/test.cwl b/progs/unit_tests/test_sqn2gbent/test.cwl index b0f822d..744c3db 100755 --- a/progs/unit_tests/test_sqn2gbent/test.cwl +++ b/progs/unit_tests/test_sqn2gbent/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_std_validation/test.cwl b/progs/unit_tests/test_std_validation/test.cwl index a281eea..8a0290b 100755 --- a/progs/unit_tests/test_std_validation/test.cwl +++ b/progs/unit_tests/test_std_validation/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: diff --git a/progs/unit_tests/test_trnascan_wnode/test.cwl b/progs/unit_tests/test_trnascan_wnode/test.cwl index 4fcdfaa..bd41568 100644 --- a/progs/unit_tests/test_trnascan_wnode/test.cwl +++ b/progs/unit_tests/test_trnascan_wnode/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "trnascan_wnode" class: Workflow diff --git a/progs/unit_tests/test_univ_prot_stats/test.cwl b/progs/unit_tests/test_univ_prot_stats/test.cwl index 55758f6..c9c2154 100755 --- a/progs/unit_tests/test_univ_prot_stats/test.cwl +++ b/progs/unit_tests/test_univ_prot_stats/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_val_format/test.cwl b/progs/unit_tests/test_val_format/test.cwl index d491a28..6ed7d43 100644 --- a/progs/unit_tests/test_val_format/test.cwl +++ b/progs/unit_tests/test_val_format/test.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "val_format" class: Workflow diff --git a/progs/unit_tests/test_val_format/val_format.cwl b/progs/unit_tests/test_val_format/val_format.cwl index 2e92a87..9e8b566 100644 --- a/progs/unit_tests/test_val_format/val_format.cwl +++ b/progs/unit_tests/test_val_format/val_format.cwl @@ -1,5 +1,5 @@ label: "val_format" -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool # these guys were not tested yet: # ncbi/gpdev 2018-06-07.prod.build138 9c0cc08e797d 42 hours ago 1.25GB diff --git a/progs/unit_tests/test_val_stats/test.cwl b/progs/unit_tests/test_val_stats/test.cwl index 3e54e77..3bc363c 100755 --- a/progs/unit_tests/test_val_stats/test.cwl +++ b/progs/unit_tests/test_val_stats/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/unit_tests/test_xml_evaluate/test.cwl b/progs/unit_tests/test_xml_evaluate/test.cwl index 6c4a637..6430e53 100755 --- a/progs/unit_tests/test_xml_evaluate/test.cwl +++ b/progs/unit_tests/test_xml_evaluate/test.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "xml_evaluate" class: Workflow diff --git a/progs/unit_tests/test_xsltproc/test.cwl b/progs/unit_tests/test_xsltproc/test.cwl index bcf6d1f..9272b72 100755 --- a/progs/unit_tests/test_xsltproc/test.cwl +++ b/progs/unit_tests/test_xsltproc/test.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/progs/univec_wnode.cwl b/progs/univec_wnode.cwl index 4c5101e..35cdcba 100644 --- a/progs/univec_wnode.cwl +++ b/progs/univec_wnode.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0 +cwlVersion: v1.2 $namespaces: sbg: 'https://www.sevenbridges.com/' id: univec_wnode diff --git a/progs/val_format.cwl b/progs/val_format.cwl index 0b912b6..7ce3128 100644 --- a/progs/val_format.cwl +++ b/progs/val_format.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "val_format" class: CommandLineTool diff --git a/progs/val_stats.cwl b/progs/val_stats.cwl index 6e228d7..dd1c3bc 100644 --- a/progs/val_stats.cwl +++ b/progs/val_stats.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "val_stats" class: CommandLineTool diff --git a/progs/xml_evaluate.cwl b/progs/xml_evaluate.cwl index 6f1548d..824d2c6 100644 --- a/progs/xml_evaluate.cwl +++ b/progs/xml_evaluate.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: xml_evaluate class: CommandLineTool baseCommand: xml_evaluate diff --git a/progs/xsltproc.cwl b/progs/xsltproc.cwl index 51a49a2..114b591 100644 --- a/progs/xsltproc.cwl +++ b/progs/xsltproc.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "xsltproc" class: CommandLineTool diff --git a/progs/yaml2json.cwl b/progs/yaml2json.cwl index ff53d9d..a0a8b6e 100644 --- a/progs/yaml2json.cwl +++ b/progs/yaml2json.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "yaml2json" class: CommandLineTool baseCommand: yaml2json.py diff --git a/protein_alignment/align_filter.cwl b/protein_alignment/align_filter.cwl index 3eabaf6..373bb6e 100644 --- a/protein_alignment/align_filter.cwl +++ b/protein_alignment/align_filter.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Filter Protein Alignments" diff --git a/protein_alignment/align_sort.cwl b/protein_alignment/align_sort.cwl index c3c1a3a..39c18b5 100644 --- a/protein_alignment/align_sort.cwl +++ b/protein_alignment/align_sort.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Sort Seed Hits, align_sort" diff --git a/protein_alignment/bacterial_prot_src.cwl b/protein_alignment/bacterial_prot_src.cwl index 12d5477..7e12f49 100644 --- a/protein_alignment/bacterial_prot_src.cwl +++ b/protein_alignment/bacterial_prot_src.cwl @@ -1,6 +1,6 @@ #!/usr/bin/ent cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Get Proteins, bacterial_prot_src" diff --git a/protein_alignment/bacterial_protalign_filter.cwl b/protein_alignment/bacterial_protalign_filter.cwl index 19f9e7e..65ba7ff 100644 --- a/protein_alignment/bacterial_protalign_filter.cwl +++ b/protein_alignment/bacterial_protalign_filter.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Filter Full-Coverage Alignments" diff --git a/protein_alignment/cat.cwl b/protein_alignment/cat.cwl index f2d64b5..9587ef4 100644 --- a/protein_alignment/cat.cwl +++ b/protein_alignment/cat.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "file concatenation" diff --git a/protein_alignment/cut_job_path.cwl b/protein_alignment/cut_job_path.cwl index 1b2f392..41e79b6 100644 --- a/protein_alignment/cut_job_path.cwl +++ b/protein_alignment/cut_job_path.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "make path relative in a worker node job file" diff --git a/protein_alignment/gpx_make_outputs.cwl b/protein_alignment/gpx_make_outputs.cwl index 5a6cbf6..a4e0ba2 100644 --- a/protein_alignment/gpx_make_outputs.cwl +++ b/protein_alignment/gpx_make_outputs.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Seed Protein Alignments, gather" diff --git a/protein_alignment/gpx_qdump.cwl b/protein_alignment/gpx_qdump.cwl index 0f5553e..5c323fe 100644 --- a/protein_alignment/gpx_qdump.cwl +++ b/protein_alignment/gpx_qdump.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Seed Search Compartments, gather" diff --git a/protein_alignment/gpx_qdump_pro.cwl b/protein_alignment/gpx_qdump_pro.cwl index 1b3b75b..6ae1f1a 100644 --- a/protein_alignment/gpx_qdump_pro.cwl +++ b/protein_alignment/gpx_qdump_pro.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Find ProSplign Alignments, gather" diff --git a/protein_alignment/gpx_qsubmit.cwl b/protein_alignment/gpx_qsubmit.cwl index 032d749..2031159 100644 --- a/protein_alignment/gpx_qsubmit.cwl +++ b/protein_alignment/gpx_qsubmit.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Seed Search Compartments, scatter" diff --git a/protein_alignment/gpx_qsubmit_1.cwl b/protein_alignment/gpx_qsubmit_1.cwl index f1f5b7f..11666b5 100644 --- a/protein_alignment/gpx_qsubmit_1.cwl +++ b/protein_alignment/gpx_qsubmit_1.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Seed Protein Alignments, scatter" diff --git a/protein_alignment/gpx_qsubmit_pro.cwl b/protein_alignment/gpx_qsubmit_pro.cwl index 039bc9b..54f6749 100644 --- a/protein_alignment/gpx_qsubmit_pro.cwl +++ b/protein_alignment/gpx_qsubmit_pro.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Find ProSplign Alignments, scatter" diff --git a/protein_alignment/prosplign_compart.cwl b/protein_alignment/prosplign_compart.cwl index 603af74..93f8fe5 100644 --- a/protein_alignment/prosplign_compart.cwl +++ b/protein_alignment/prosplign_compart.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Filter Protein Seeds, compart" diff --git a/protein_alignment/prosplign_compart_filter.cwl b/protein_alignment/prosplign_compart_filter.cwl index b1e7640..0f00e0f 100644 --- a/protein_alignment/prosplign_compart_filter.cwl +++ b/protein_alignment/prosplign_compart_filter.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Filter Protein Seeds, compart filter" diff --git a/protein_alignment/prosplign_wnode.cwl b/protein_alignment/prosplign_wnode.cwl index e4b6f70..0905868 100644 --- a/protein_alignment/prosplign_wnode.cwl +++ b/protein_alignment/prosplign_wnode.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Seed Search Compartments, execute" diff --git a/protein_alignment/tblastn_wnode.cwl b/protein_alignment/tblastn_wnode.cwl index 6602568..e14b337 100644 --- a/protein_alignment/tblastn_wnode.cwl +++ b/protein_alignment/tblastn_wnode.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Seed Search Compartments, execute" diff --git a/protein_alignment/tblastn_wnode_1.cwl b/protein_alignment/tblastn_wnode_1.cwl index f0ecc45..30b02e6 100644 --- a/protein_alignment/tblastn_wnode_1.cwl +++ b/protein_alignment/tblastn_wnode_1.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "Seed Protein Alignments, execute" diff --git a/protein_alignment/wf_align_filter.cwl b/protein_alignment/wf_align_filter.cwl index 0b67e7a..3acbe75 100644 --- a/protein_alignment/wf_align_filter.cwl +++ b/protein_alignment/wf_align_filter.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "Filter Protein Alignments" diff --git a/protein_alignment/wf_compart_filter_prosplign.cwl b/protein_alignment/wf_compart_filter_prosplign.cwl index 8e622f0..92ef5a1 100644 --- a/protein_alignment/wf_compart_filter_prosplign.cwl +++ b/protein_alignment/wf_compart_filter_prosplign.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "Filter Protein Seeds; Find ProSplign Alignments" diff --git a/protein_alignment/wf_protein_alignment.cwl b/protein_alignment/wf_protein_alignment.cwl index e4c2ddd..35dc9f9 100755 --- a/protein_alignment/wf_protein_alignment.cwl +++ b/protein_alignment/wf_protein_alignment.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "Align reference proteins plane complete workflow" diff --git a/protein_alignment/wf_seed.cwl b/protein_alignment/wf_seed.cwl index cfcb138..757cf1a 100644 --- a/protein_alignment/wf_seed.cwl +++ b/protein_alignment/wf_seed.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "Seed Search Compartments" diff --git a/protein_alignment/wf_seed_1.cwl b/protein_alignment/wf_seed_1.cwl index a97c3bd..1655ac4 100644 --- a/protein_alignment/wf_seed_1.cwl +++ b/protein_alignment/wf_seed_1.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "Seed Protein Alignments" diff --git a/split_jobs/cat_array_of_files.cwl b/split_jobs/cat_array_of_files.cwl index cb4d050..29d5bb2 100644 --- a/split_jobs/cat_array_of_files.cwl +++ b/split_jobs/cat_array_of_files.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "file concatenation" diff --git a/split_jobs/split.cwl b/split_jobs/split.cwl index cea0d6c..b8957d2 100644 --- a/split_jobs/split.cwl +++ b/split_jobs/split.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: "cwl split wrapper" diff --git a/spurious_annot/wf_spurious_annot_pass1.cwl b/spurious_annot/wf_spurious_annot_pass1.cwl index 66247b3..92952ea 100644 --- a/spurious_annot/wf_spurious_annot_pass1.cwl +++ b/spurious_annot/wf_spurious_annot_pass1.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: spurious_annot -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: - class: SubworkflowFeatureRequirement diff --git a/spurious_annot/wf_spurious_annot_pass2.cwl b/spurious_annot/wf_spurious_annot_pass2.cwl index 7e7727c..3083b02 100644 --- a/spurious_annot/wf_spurious_annot_pass2.cwl +++ b/spurious_annot/wf_spurious_annot_pass2.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: "spurious_annot pass2" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: - class: SubworkflowFeatureRequirement diff --git a/task_types/tt_align_filter_sa.cwl b/task_types/tt_align_filter_sa.cwl index 0965e0e..39e8fc8 100644 --- a/task_types/tt_align_filter_sa.cwl +++ b/task_types/tt_align_filter_sa.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "align_filter_sa" class: Workflow # task type requirements: diff --git a/task_types/tt_align_merge_sas.cwl b/task_types/tt_align_merge_sas.cwl index 3de1280..9e3a28f 100644 --- a/task_types/tt_align_merge_sas.cwl +++ b/task_types/tt_align_merge_sas.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "align_merge_sas" class: Workflow # task type inputs: diff --git a/task_types/tt_align_sort_sa.cwl b/task_types/tt_align_sort_sa.cwl index 0987c17..7de0ba7 100644 --- a/task_types/tt_align_sort_sa.cwl +++ b/task_types/tt_align_sort_sa.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "align_sort_sa" class: Workflow # task type inputs: diff --git a/task_types/tt_ani_top_n.cwl b/task_types/tt_ani_top_n.cwl index 87fef24..90752f9 100644 --- a/task_types/tt_ani_top_n.cwl +++ b/task_types/tt_ani_top_n.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "ani_top_n" # file: task_types/tt_ani_top_n.cwl class: Workflow # task type diff --git a/task_types/tt_assm_assm_blastn_wnode.cwl b/task_types/tt_assm_assm_blastn_wnode.cwl index 5e097f1..7929c2e 100644 --- a/task_types/tt_assm_assm_blastn_wnode.cwl +++ b/task_types/tt_assm_assm_blastn_wnode.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "assm_assm_blastn_wnode" class: Workflow # task type inputs: diff --git a/task_types/tt_bact_get_kmer_reference.cwl b/task_types/tt_bact_get_kmer_reference.cwl index ef8e70d..d8e1a2d 100644 --- a/task_types/tt_bact_get_kmer_reference.cwl +++ b/task_types/tt_bact_get_kmer_reference.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "bact_get_kmer_reference" # File: task_types/tt_bact_get_kmer_reference.cwl class: Workflow # task type diff --git a/task_types/tt_blastn_wnode.cwl b/task_types/tt_blastn_wnode.cwl index 77a21fd..eae5589 100644 --- a/task_types/tt_blastn_wnode.cwl +++ b/task_types/tt_blastn_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "tt_blastn_wnode" class: Workflow # task type requirements: diff --git a/task_types/tt_blastp_wnode_naming.cwl b/task_types/tt_blastp_wnode_naming.cwl index 90651dc..9095f7d 100644 --- a/task_types/tt_blastp_wnode_naming.cwl +++ b/task_types/tt_blastp_wnode_naming.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "blastp_wnode_naming" class: Workflow # task type requirements: diff --git a/task_types/tt_blastp_wnode_struct.cwl b/task_types/tt_blastp_wnode_struct.cwl index 2775392..d286fe6 100644 --- a/task_types/tt_blastp_wnode_struct.cwl +++ b/task_types/tt_blastp_wnode_struct.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "blastp_wnode_struct" class: Workflow # task type requirements: diff --git a/task_types/tt_cache_asnb_entries.cwl b/task_types/tt_cache_asnb_entries.cwl index 7cab0d0..ab16565 100644 --- a/task_types/tt_cache_asnb_entries.cwl +++ b/task_types/tt_cache_asnb_entries.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "cache_asnb_entries" class: Workflow # task type inputs: diff --git a/task_types/tt_cluster_and_qdump.cwl b/task_types/tt_cluster_and_qdump.cwl index b0c7b72..0d97276 100644 --- a/task_types/tt_cluster_and_qdump.cwl +++ b/task_types/tt_cluster_and_qdump.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow diff --git a/task_types/tt_extract_gencoll_ids.cwl b/task_types/tt_extract_gencoll_ids.cwl index 07d76cf..00f380d 100644 --- a/task_types/tt_extract_gencoll_ids.cwl +++ b/task_types/tt_extract_gencoll_ids.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: extract_gencoll_ids # File: tt_extract_gencoll_ids.cwl class: Workflow # task type diff --git a/task_types/tt_format_rrnas_from_seq_entry.cwl b/task_types/tt_format_rrnas_from_seq_entry.cwl index 9e951f2..e2e0e7f 100644 --- a/task_types/tt_format_rrnas_from_seq_entry.cwl +++ b/task_types/tt_format_rrnas_from_seq_entry.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "format_rrnas_from_seq_entry" class: Workflow # task type inputs: diff --git a/task_types/tt_fscr_calls_pass1.cwl b/task_types/tt_fscr_calls_pass1.cwl index 1510dd7..f1ed404 100644 --- a/task_types/tt_fscr_calls_pass1.cwl +++ b/task_types/tt_fscr_calls_pass1.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "tt_fscr_calls_pass1" class: Workflow # task type inputs: diff --git a/task_types/tt_gcaccess_from_list.cwl b/task_types/tt_gcaccess_from_list.cwl index 012fd55..93a1758 100644 --- a/task_types/tt_gcaccess_from_list.cwl +++ b/task_types/tt_gcaccess_from_list.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "gcaccess_from_list" # File: task+types/tt_gcaccess_from_list.cwl class: Workflow # task type diff --git a/task_types/tt_hmmsearch_wnode.cwl b/task_types/tt_hmmsearch_wnode.cwl index 65f2576..6e81782 100644 --- a/task_types/tt_hmmsearch_wnode.cwl +++ b/task_types/tt_hmmsearch_wnode.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/task_types/tt_hmmsearch_wnode_plus_qdump.cwl b/task_types/tt_hmmsearch_wnode_plus_qdump.cwl index 809454f..49eca98 100644 --- a/task_types/tt_hmmsearch_wnode_plus_qdump.cwl +++ b/task_types/tt_hmmsearch_wnode_plus_qdump.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow diff --git a/task_types/tt_kmer_build_tree.cwl b/task_types/tt_kmer_build_tree.cwl index 2a4d9f7..9e1ad79 100644 --- a/task_types/tt_kmer_build_tree.cwl +++ b/task_types/tt_kmer_build_tree.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: kmer_build_tree class: Workflow # task type inputs: diff --git a/task_types/tt_kmer_cache_retrieve.cwl b/task_types/tt_kmer_cache_retrieve.cwl index 4dc5bb1..19f7ab0 100644 --- a/task_types/tt_kmer_cache_retrieve.cwl +++ b/task_types/tt_kmer_cache_retrieve.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_cache_retrieve" # file: task_types/tt_kmer_cache_retrieve.cwl class: Workflow # task type diff --git a/task_types/tt_kmer_cache_store.cwl b/task_types/tt_kmer_cache_store.cwl index 8e7031c..da0d7e1 100644 --- a/task_types/tt_kmer_cache_store.cwl +++ b/task_types/tt_kmer_cache_store.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_cache_store" # file: task_types/tt_kmer_cache_store.cwl class: Workflow # task type diff --git a/task_types/tt_kmer_compare_wnode.cwl b/task_types/tt_kmer_compare_wnode.cwl index 48c37c4..70d9284 100644 --- a/task_types/tt_kmer_compare_wnode.cwl +++ b/task_types/tt_kmer_compare_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "tt_kmer_compare_wnode" doc: 'Pairwise comparison' # File: tt_kmer_compare_wnode.cwl diff --git a/task_types/tt_kmer_gc_extract_wnode.cwl b/task_types/tt_kmer_gc_extract_wnode.cwl index 7c7d5ad..73c03fb 100644 --- a/task_types/tt_kmer_gc_extract_wnode.cwl +++ b/task_types/tt_kmer_gc_extract_wnode.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_gc_extract_wnode" # File "task_types/tt_kmer_gc_extract_wnode.cwl" # caller steps: diff --git a/task_types/tt_kmer_ref_compare_wnode.cwl b/task_types/tt_kmer_ref_compare_wnode.cwl index 72ba3ae..f59ee46 100644 --- a/task_types/tt_kmer_ref_compare_wnode.cwl +++ b/task_types/tt_kmer_ref_compare_wnode.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_ref_compare_wnode" class: Workflow # task type inputs: diff --git a/task_types/tt_kmer_seq_entry_extract_wnode.cwl b/task_types/tt_kmer_seq_entry_extract_wnode.cwl index b1b36ec..3decbf9 100644 --- a/task_types/tt_kmer_seq_entry_extract_wnode.cwl +++ b/task_types/tt_kmer_seq_entry_extract_wnode.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_seq_entry_extract_wnode" class: Workflow # task type inputs: diff --git a/task_types/tt_kmer_top_n.cwl b/task_types/tt_kmer_top_n.cwl index dc05b5c..80b1d36 100644 --- a/task_types/tt_kmer_top_n.cwl +++ b/task_types/tt_kmer_top_n.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow # task type # kmer_top_identification -N 20 -distances-manifest kmer_top_n.455674842/inp/distances.mft \ # -omatches kmer_top_n.455674842/tmp/matches \ diff --git a/task_types/tt_kmer_top_n_extract.cwl b/task_types/tt_kmer_top_n_extract.cwl index 6de1949..c46b36d 100644 --- a/task_types/tt_kmer_top_n_extract.cwl +++ b/task_types/tt_kmer_top_n_extract.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "kmer_top_n_extract" # file: tt_kmer_top_n_extract.cwl class: Workflow # task type diff --git a/task_types/tt_preserve_annot.cwl b/task_types/tt_preserve_annot.cwl index 4e204ab..bee1bac 100644 --- a/task_types/tt_preserve_annot.cwl +++ b/task_types/tt_preserve_annot.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: preserve_annot arguments: [ -nogenbank ] diff --git a/task_types/tt_taxonomy_check_16S.cwl b/task_types/tt_taxonomy_check_16S.cwl index b9c66dd..8ca2f09 100644 --- a/task_types/tt_taxonomy_check_16S.cwl +++ b/task_types/tt_taxonomy_check_16S.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 label: "taxonomy_check_16S" class: Workflow # task type inputs: diff --git a/task_types/tt_univec_wnode.cwl b/task_types/tt_univec_wnode.cwl index fe6cef7..ce2dbd5 100644 --- a/task_types/tt_univec_wnode.cwl +++ b/task_types/tt_univec_wnode.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.0 +cwlVersion: v1.2 id: tt_univec_wnode doc: univ_wnode label: univec_wnode diff --git a/taxcheck.cwl b/taxcheck.cwl index 2828f39..fde7f18 100755 --- a/taxcheck.cwl +++ b/taxcheck.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0 +cwlVersion: v1.2 doc: | Perform taxonomic identification tasks on an input genome requirements: diff --git a/taxonomy_check_16S/wf_taxonomy_check_16S.cwl b/taxonomy_check_16S/wf_taxonomy_check_16S.cwl index 6be38da..9709422 100644 --- a/taxonomy_check_16S/wf_taxonomy_check_16S.cwl +++ b/taxonomy_check_16S/wf_taxonomy_check_16S.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner label: taxonomy_check_16S -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: - class: SubworkflowFeatureRequirement diff --git a/vecscreen/bacterial_screening.cwl b/vecscreen/bacterial_screening.cwl index f15b8e3..7e42b62 100644 --- a/vecscreen/bacterial_screening.cwl +++ b/vecscreen/bacterial_screening.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.0 +cwlVersion: v1.2 id: bacterial_screening label: bacterial_screening requirements: diff --git a/vecscreen/foreign_screening.cwl b/vecscreen/foreign_screening.cwl index e919527..2c270fa 100644 --- a/vecscreen/foreign_screening.cwl +++ b/vecscreen/foreign_screening.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.0 +cwlVersion: v1.2 id: foreign_screening label: foreign_screening requirements: diff --git a/vecscreen/vecscreen.cwl b/vecscreen/vecscreen.cwl index fa87bad..99ad2a5 100644 --- a/vecscreen/vecscreen.cwl +++ b/vecscreen/vecscreen.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.0 +cwlVersion: v1.2 id: vecscreen label: vecscreen requirements: diff --git a/wf_bacterial_prot_src.cwl b/wf_bacterial_prot_src.cwl index b8592fe..2269998 100644 --- a/wf_bacterial_prot_src.cwl +++ b/wf_bacterial_prot_src.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: "Get Proteins" diff --git a/wf_common.cwl b/wf_common.cwl index 2a34eb5..2f96f71 100755 --- a/wf_common.cwl +++ b/wf_common.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow doc: PGAP pipeline for external usage, powered via containers diff --git a/wf_pgap_simple.cwl b/wf_pgap_simple.cwl index 4ec4716..4e4dcc1 100755 --- a/wf_pgap_simple.cwl +++ b/wf_pgap_simple.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner label: "PGAP Pipeline, simple user input" -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow doc: | PGAP pipeline for external usage, powered via containers,