Workflow: PGAP Pipeline
Fetched 2025-10-22 21:09:46 GMT
Verified with cwltool version 3.1.20230201224320
PGAP pipeline for external usage, powered via containers
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/pgap/ed27a47e80a85c76cb7285a78965d59537f79f10/LICENSE.md
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| go | Boolean[] | ||
| taxid | Integer | ||
| dbname | String (Optional) | ||
| entries | File (Optional) | ||
| uuid_in | File (Optional) | ||
| make_uuid | Boolean (Optional) | ||
| os_version | String (Optional) | ||
| seq_submit | File (Optional) | ||
| no_internet | Boolean (Optional) | ||
| gc_assm_name | String | ||
| report_usage | Boolean | ||
| locus_tag_prefix | String (Optional) | ||
| ignore_all_errors | Boolean (Optional) | ||
| submol_block_json | File | ||
| supplemental_data | Directory | ||
| blast_hits_cache_data | Directory (Optional) | ||
| scatter_gather_nchunks | String | ||
| xpath_fail_final_asndisc | String (Optional) |
The default: setting is for standard call of pgap.cwl (for example, from pgap.py) |
|
| contact_as_author_possible | Boolean (Optional) | ||
| xpath_fail_initial_asndisc | String (Optional) |
The default: setting is for standard call of pgap.cwl (for example, from pgap.py) |
|
| xpath_fail_final_asnvalidate | String (Optional) |
The default: setting is for standard call of pgap.cwl (for example, from pgap.py) |
|
| xpath_fail_initial_asnvalidate | String (Optional) |
The default: setting is for standard call of pgap.cwl (for example, from pgap.py) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| checkm |
checkm/wf_checkm.cwl
(Workflow)
|
checkm | |
| passdata |
expr/supplemental_data_split_dir.cwl
(ExpressionTool)
|
Split input directory into subpath flows | |
| orfs_hmms |
bacterial_annot/wf_orf_hmms.cwl
(Workflow)
|
Bacterial Annotation, pass 1, genemark training, by HMMs (first pass) | |
| ping_stop |
progs/pinger.cwl
(CommandLineTool)
|
pinger | |
| ping_start |
progs/pinger.cwl
(CommandLineTool)
|
pinger | |
| Get_Proteins |
wf_bacterial_prot_src.cwl
(Workflow)
|
Get Proteins | |
| Add_Locus_Tags |
progs/add_locus_tags.cwl
(CommandLineTool)
|
add_locus_tags | |
| bacterial_trna |
bacterial_trna/wf_trnascan.cwl
(Workflow)
|
Run tRNAScan | |
| genomic_source |
genomic_source/wf_genomic_source_asn.cwl
(Workflow)
|
Create Genomic Collection for Bacterial Pipeline, ASN.1 input | |
| bacterial_ncrna |
bacterial_ncrna/wf_gcmsearch.cwl
(Workflow)
|
Run genomic CMsearch (Rfam rRNA) | |
| add_checksum_sqn |
progs/annot_checksum.cwl
(CommandLineTool)
|
||
| Cache_Entrez_Gene |
cache_entrez_gene.cwl
(CommandLineTool)
|
Cache Entrez Gene | |
| ab_initio_antifam |
bacterial_annot/wf_ab_initio_antifam.cwl
(Workflow)
|
Bacterial Annotation, ab initio (first pass) searched against AntiFam | |
| protein_alignment | Align reference proteins plane complete workflow, with miniprot | ||
| ab_initio_training |
bacterial_annot/wf_ab_initio_training.cwl
(Workflow)
|
Bacterial Annotation, pass 1, genemark training, by HMMs (first pass) | |
| add_checksum_gbent |
progs/annot_checksum.cwl
(CommandLineTool)
|
||
| bacterial_noncoding | Non-Coding Bacterial Genes | ||
| genus_list_file2ints |
progs/file2ints.cwl
(ExpressionTool)
|
||
| log_package_versions |
progs/catlog.cwl
(CommandLineTool)
|
concatenates input File[] to screen |
|
| spurious_annot_final |
spurious_annot/wf_spurious_annot_pass2.cwl
(Workflow)
|
spurious_annot pass2 | |
| bacterial_mobile_elem | Execute CRISPR | ||
| spurious_annot_prelim |
spurious_annot/wf_spurious_annot_pass1.cwl
(Workflow)
|
spurious_annot | |
| Create_Genomic_BLASTdb |
progs/gp_makeblastdb.cwl
(Workflow)
|
gp_makeblastdb | |
| bacterial_annot_1st_pass |
bacterial_annot/wf_bacterial_annot_pass2.cwl
(Workflow)
|
Bacterial Annotation, pass 2, blastp-based functional annotation (first pass) | |
| Get_Order_Specific_Strings |
progs/file2basenames.cwl
(ExpressionTool)
|
||
| Prepare_Unannotated_Sequences |
bacterial_prepare_unannotated.cwl
(CommandLineTool)
|
Prepare Unannotated Sequences |
Prepare Unannotated Sequences |
| Final_Bacterial_Package_ent2sqn |
progs/ent2sqn.cwl
(CommandLineTool)
|
ent2sqn | |
| Generate_Annotation_Reports_gbk |
progs/asn2flat.cwl
(CommandLineTool)
|
asn2flat | |
| Generate_Annotation_Reports_gff |
progs/gp_annot_format.cwl
(CommandLineTool)
|
gp_annot_format | |
| bacterial_annot_2nd_pass_blastp |
bacterial_annot/wf_bacterial_annot_pass4.cwl
(Workflow)
|
Bacterial Annotation, pass 4, blastp-based functional annotation (second pass) | |
| bacterial_orthology_conditional | bacterial_orthology_cond | ||
| blast_hits_cache_data_split_dir |
expr/blast_hits_cache_data_split_dir.cwl
(ExpressionTool)
|
Split input directory into subpath flows | |
| Final_Bacterial_Package_sqn2gbent |
progs/sqn2gbent.cwl
(CommandLineTool)
|
sqn2gbent | |
| Final_Bacterial_Package_val_stats |
progs/val_stats.cwl
(CommandLineTool)
|
val_stats | |
| bacterial_annot_2nd_pass_genemark | Bacterial Annotation, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass) | ||
| Prepare_Unannotated_Sequences_text |
progs/asn_translator.cwl
(CommandLineTool)
|
asn_translator | |
| Final_Bacterial_Package_asn_cleanup |
progs/asn_cleanup.cwl
(CommandLineTool)
|
asn_cleanup | |
| Validate_Annotation_proc_annot_stats |
progs/proc_annot_stats.cwl
(CommandLineTool)
|
proc_annot_stats | |
| Validate_Annotation_xsltproc_asndisc |
progs/xsltproc.cwl
(CommandLineTool)
|
xsltproc | |
| Generate_Annotation_Reports_nuc_fasta |
progs/asn2fasta.cwl
(CommandLineTool)
|
asn2fasta | |
| Final_Bacterial_Package_final_bact_asn |
progs/final_bact_asn.cwl
(CommandLineTool)
|
final_bact_asn | |
| Final_Bacterial_Package_std_validation |
progs/std_validation.cwl
(CommandLineTool)
|
std_validation | |
| Generate_Annotation_Reports_prot_fasta |
progs/asn2fasta.cwl
(CommandLineTool)
|
asn2fasta | |
| Validate_Annotation_collect_annot_stats |
progs/collect_annot_stats.cwl
(CommandLineTool)
|
collect_annot_stats | |
| Final_Bacterial_Package_asndisc_evaluate |
progs/xml_evaluate.cwl
(CommandLineTool)
|
xml_evaluate | |
| Validate_Annotation_bact_univ_prot_stats |
progs/bact_univ_prot_stats.cwl
(CommandLineTool)
|
bact_univ_prot_stats | |
| Validate_Annotation_xsltproc_asnvalidate |
progs/xsltproc.cwl
(CommandLineTool)
|
xsltproc | |
| Generate_Annotation_Reports_cds_nuc_fasta |
progs/asn2fasta.cwl
(CommandLineTool)
|
asn2fasta | |
| Prepare_Unannotated_Sequences_asndisc_cpp |
progs/asndisc_cpp.cwl
(CommandLineTool)
|
asndisc_cpp | |
| Prepare_Unannotated_Sequences_asnvalidate |
progs/asnvalidate.cwl
(CommandLineTool)
|
asnvalidate | |
| Validate_Annotation_collect_annot_details |
progs/collect_annot_stats.cwl
(CommandLineTool)
|
collect_annot_stats | |
| Generate_Annotation_Reports_cds_prot_fasta |
progs/asn2fasta.cwl
(CommandLineTool)
|
asn2fasta | |
| Final_Bacterial_Package_asnvalidate_evaluate |
progs/xml_evaluate.cwl
(CommandLineTool)
|
xml_evaluate | |
| Final_Bacterial_Package_dumb_down_as_required |
progs/dumb_down_as_required.cwl
(CommandLineTool)
|
dumb_down_as_required | |
| Prepare_Unannotated_Sequences_asndisc_evaluate |
progs/xml_evaluate.cwl
(CommandLineTool)
|
xml_evaluate | |
| Prepare_Unannotated_Sequences_pgapx_input_check |
progs/pgapx_input_check.cwl
(CommandLineTool)
|
pgapx_input_check | |
| Prepare_Unannotated_Sequences_asnvalidate_evaluate |
progs/xml_evaluate.cwl
(CommandLineTool)
|
xml_evaluate |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gbk | File | ||
| gff | File | ||
| sqn | File | ||
| gbent | File | ||
| checkm_raw | File | ||
| protein_fasta | File (Optional) | ||
| checkm_results | File | ||
| nucleotide_fasta | File (Optional) | ||
| proc_annot_stats | File | ||
| cds_protein_fasta | File (Optional) | ||
| all_proc_annot_stats | File | ||
| cds_nucleotide_fasta | File (Optional) | ||
| final_asnval_error_diag | File (Optional) | ||
| final_asndisc_error_diag | File (Optional) | ||
| initial_asnval_error_diag | File (Optional) | ||
| initial_asndisc_error_diag | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/ed27a47e80a85c76cb7285a78965d59537f79f10/wf_common.cwl
