Workflow: PGAP Pipeline
Fetched 2023-01-04 23:52:08 GMT
Verified with cwltool version 3.1.20221201130942
PGAP pipeline for external usage, powered via Docker 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-gpipe/pgap/c08fd46e8f715b9b5aa487466705863e4b1829df/GeneMarkS_Software_License.txt
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fasta | File | ||
| taxid | Integer | ||
| dbname | String (Optional) | ||
| CDDdata | Directory | ||
| CDDdata2 | Directory | ||
| hmm_path | Directory | ||
| hmms_tab | File | ||
| taxon_db | File | ||
| wp_hashes | File | ||
| AntiFamLib | Directory | ||
| thresholds | File | ||
| asn2pas_xsl | File | ||
| gc_assm_name | String | ||
| 5s_model_path | File | ||
| genemark_path | Directory | ||
| naming_sqlite | File | ||
| uniColl_cache | Directory | ||
| univ_prot_xml | File | ||
| blast_rules_db | String | ||
| rfam_stockholm | File | ||
| selenoproteins | Directory | ||
| 16s_blastdb_dir | Directory | ||
| 23s_blastdb_dir | Directory | ||
| gene_master_ini | File | ||
| naming_blast_db | Directory | ||
| naming_hmms_tab | File | ||
| rfam_amendments | File | ||
| rfam_model_path | File | ||
| val_res_den_xml | File | ||
| locus_tag_prefix | String (Optional) | ||
| blast_rules_db_dir | Directory | ||
| naming_hmms_combined | Directory | ||
| defline_cleanup_rules | File | ||
| submit_block_template | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| 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.cwl
(Workflow)
|
Create Genomic Collection for Bacterial Pipeline | |
| 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) | |
| 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 | |
| bacterial_noncoding | Non-Coding Bacterial Genes | ||
| 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 |
Note that this implementation skips asn validation steps. Please fix |
| 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 | |
| Final_Bacterial_Package_sqn2gbent |
progs/sqn2gbent.cwl
(CommandLineTool)
|
sqn2gbent | |
| Final_Bacterial_Package_val_stats |
progs/val_stats.cwl
(CommandLineTool)
|
val_stats | |
| 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 | |
| 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 | |
| Validate_Annotation_collect_annot_details |
progs/collect_annot_stats.cwl
(CommandLineTool)
|
collect_annot_stats | |
| Final_Bacterial_Package_dumb_down_as_required |
progs/dumb_down_as_required.cwl
(CommandLineTool)
|
dumb_down_as_required |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gbk | File | ||
| gff | File | ||
| gbent | File | ||
| protein_fasta | File (Optional) | ||
| nucleotide_fasta | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/c08fd46e8f715b9b5aa487466705863e4b1829df/wf_pgap.cwl
