Workflow: PGAP Pipeline
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/1a6b9e5dea09caa0debbaff30ca39005dfa5e4d4/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) | ||
seq_submit | File (Optional) | ||
no_internet | Boolean (Optional) | ||
gc_assm_name | String | ||
report_usage | Boolean | ||
blast_rules_db | String | ||
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 |
---|---|---|---|
passdata |
expr/supplemental_data_split_dir.cwl
(ExpressionTool)
|
Split input directory into subpath flows | |
ping_stop |
progs/pinger.cwl
(CommandLineTool)
|
pinger | |
ping_start |
progs/pinger.cwl
(CommandLineTool)
|
pinger | |
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_annot |
bacterial_annot/wf_bacterial_annot_pass1.cwl
(Workflow)
|
Bacterial Annotation, pass 1, genemark training, by HMMs (first pass) | |
bacterial_ncrna |
bacterial_ncrna/wf_gcmsearch.cwl
(Workflow)
|
Run genomic CMsearch (Rfam rRNA) | |
add_checksum_sqn |
progs/annot_checksum.cwl
(CommandLineTool)
|
||
spurious_annot_1 |
spurious_annot/wf_spurious_annot_pass1.cwl
(Workflow)
|
spurious_annot | |
spurious_annot_2 |
spurious_annot/wf_spurious_annot_pass2.cwl
(Workflow)
|
spurious_annot pass2 | |
Cache_Entrez_Gene |
cache_entrez_gene.cwl
(CommandLineTool)
|
Cache Entrez Gene | |
bacterial_annot_2 |
bacterial_annot/wf_bacterial_annot_pass2.cwl
(Workflow)
|
Bacterial Annotation, pass 2, blastp-based functional annotation (first pass) | |
bacterial_annot_3 |
bacterial_annot/wf_bacterial_annot_pass3.cwl
(Workflow)
|
Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass) | |
bacterial_annot_4 |
bacterial_annot/wf_bacterial_annot_pass4.cwl
(Workflow)
|
Bacterial Annotation, pass 4, blastp-based functional annotation (second pass) | |
protein_alignment |
protein_alignment/wf_protein_alignment.cwl
(Workflow)
|
Align reference proteins plane complete workflow | |
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 |
|
bacterial_mobile_elem | Execute CRISPR | ||
Create_Genomic_BLASTdb |
progs/gp_makeblastdb.cwl
(Workflow)
|
gp_makeblastdb | |
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 | |
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 | |
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 | |
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 | |
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 | ||
protein_fasta | File (Optional) | ||
nucleotide_fasta | File (Optional) | ||
proc_annot_stats | File | ||
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/1a6b9e5dea09caa0debbaff30ca39005dfa5e4d4/wf_common.cwl