Updated description (#230)

Updated task description  from describing spatyping to describing srst2 for vibrio

Merge pull request #223 from theiagen/smw-version-update

Update version to v1.2.0

reorder snp matrix (#198)

* reorder matrix with terminal ends

* fix typo

* fix more typos

* fix silly python indentation issues

* change to breadth-first search

* undo breadth-first

* cast index/header as strings

* remove unnecessary print statement

* reroot tree

* enable phandango coloring

* add data summary option

* rename things for clarity

* syntax changes

* terrafy

* add changes to core_gene_snp

* add changes to mashtree

* debug statements added

* more debug statements

* fix syntax

* syntax + debug changes

* trying other things

* hopefully last syntax bug fix

* more debug

* escapes parentheses in searches

* terrafy

* ensure sample_id is always a string

* terrafy

* fix indentation

* changes requested

* remove unused var

* remove extra white space

* changed data_summary_sample_names to sample_names

* add cluster_name as summarized_data's output prefix

* add _contigs suffix to mashtree outputs

* correct syntax and comment

* fix typo

* remove addition of _contigs

* remove mashtree boolean from workflows

* remove _contigs suffix from terminal ends

* using sed to remove "_contigs" from tree

* remove unused var

* fix typo :(

* more remnants of past mistakes :(

* remove _contigs from the matrix too

* update version

* fix indentations

Update task_versioning.wdl (#195)

remove compression from alignment files (#134)

Merge pull request #111 from theiagen/kgl-whitespace-export-dev

Update PHBG version

New NCBI-AMRFinderPlus workflow and integration in TheiaProk_Illumina…

…_PE wf (#65)

Fixes #41, Fixes #46 

* added new task file for NCBI-amrfinderplus. passes miniwdl check but is NOT incorporated or tested in any workflows yet

* adds single task workflow NCBI-AMRFinderPlus. update dockstore.yml with new wf. added lines in task to output 4 TSV outputs from amrfinderplus

* removed comment from amrfinderplus task since it was breaking the cmd. fixed import path in wf_amrfinderplus.wdl

* changed math to make integers instead of floats so bash doesn't get upset

* update to ncbi-amrfinderplus docker image 3.10.24 and deleted some comment lines

* rename amfrfinder tas to amrfinder_nuc for nculeotide. also added maxRetries to runtime block

* added amrfinderplus outputs to export_taxon_tables inputs and output TSV header and outputs

* added amrfinderplus to wf_theiaprok_illumina_pe.wdl. Have not tested locally or in Terra yet

* added code to take in user-defined inputs or gambit_predicted_taxon to use with amrfinder --organism option

* amrfinder --organism is always used and wil feed in bash variable

* updated single task wf_amrfinderplus.wdl with new task name "amrfinderplus_nuc"

* task_amrfinderplus.wdl: added double quotes so bash conditional evaluates properly

* updated/fixed PHBG_Version to v0.4.0-dev. Also quoted echo statement so VSCode stops complaining

* added if/else for amrfinder --organism flag. if organism input is supplied by user or gambit_predicted taxon, use --organism flag. otherwise do not use --organism flag

* last grep command exits gracefully even if it finds nothing

* added new outputs for amrfinderplus task for strings with all stress, virulence, and amr genes. floated to table in addition to TSVs

* added new amrfinderplus gene names string output to single-task workflow

* removed abricate from wf_theiaprok_illumina_pe and export taxon tables task. still need to test functionality. also getting warnings in VSCode that may need addressing

* added new amrfinderplus output strings to export_taxon_tables task as well as theiaprok_illumina_pe workflow

* attempting to make new amrfinderplus string outputs optional for export_taxon_tables task

* fixed outputs for export_taxon_table

* Make amrfinderplus docker image modifiable by user

* amrfinderplus_nuc task: updated string matching for all organisms. Much easier to match genus and species with 2 words. Now redirecting STDOUT/ERR to a txt file for grepping amrfinder db version. Added new output string "amrfinder_db_version". export_taxon_table task: added new amrfinderplus_db_version to inputs & resulting TSV for export taxon table. wf_amrfinderplus.wdl: added new output amrfinderplus_db_version. wf_theiaprok_illumina_pe.wdl: updated with new amrfinderplus_db_version output

* update gambit task and output

* capture trimmomatic out

* added a missing \t in export_taxon_tables task

* round est_coverage to 2 decimal places

* update default docker

* fix syntax

* Update task_versioning.wdl

* removing redundant date capture

* remove redundant date capture

* avoid workflow/task name conflict

Co-authored-by: Sage Wright <sage.wright@theiagen.com>
Co-authored-by: kevinlibuit <kevin@libuit.com>
Co-authored-by: kevinlibuit <kevinlibuit@users.noreply.github.com>

Merge pull request #54 from theiagen/kevinlibuit-patch-2

Remove mycosnp from dockstore

TheiaProk_Illumina_PE & Directory Restructure (#38)

* Update apollo to gambit v0.3.0

* Fix syntax errors

* Add apollo se workflow

* update gambit values

* rename gambit output

* rename gambit output

* register apollo_illumina_se and gamibt_query to dockstore

* remove gambit delta output

* allow user-defined genome signature database files

* use extention to define db file names

* fix typo

* make db files required

* create db dir in pwd

* switch to quay-hosted image

* report distance to 4 digits

* Gambit 0.4 (#30)

* Fix whitespace

* Use GAMBIT database in docker image

* Output GAMBIT software version

* Rename GAMBIT outputs

* Correct name of apollo_illumina_se workflow

* Use JSON output for GAMBIT

* GAMBIT table of closest hits

* Report next most specific taxon

* align input params

* reorganize tasks

* Add species_typing tasks (#34)

* add task for ectyper

* Update task_ectyper.wdl

* Update task_ectyper.wdl

* add pmga task

* Update task_pmga.wdl

* Update task_pmga.wdl

* Create wf_pmga.wdl

* fix white space

* Update task_pmga.wdl

* Update README.md

* add task for agrvate

* add species typing tasks

* Update task_snp_dists.wdl (#35)

* Create task_mlst.wdl (#36)

* Update task_agrvate.wdl

* Update task_ectyper.wdl

* Update task_emmtyper.wdl

* Update task_hicap.wdl

* Update task_kleborate.wdl

* Update task_lissero.wdl

* Update task_meningotype.wdl

* Update task_sistr.wdl

* Update task_spatyper.wdl

* Update task_staphopiasccmec.wdl

* revert to gambit 0.3.0

* Create TheiaProk workflow

* fix wdl formatting

* fix version output

* fix apollo workflow

* Add merlin tag flow control

* fix bash syntax

* set Shigella merlin tag to Escherichia

* add merlin_magic workflow

* add ectyper outs

* add listeria and salmonella typing

* fix typos

* fix ectyper args

* adjust seqsero parser

* fix lissero args

* add kleborate to workflows

* fix seqsero2 output parsing

* update table name

* update version

* add export task

* Allow export to taxon tables (#37)

* add export taxon table task

* fix bash syntax

* remove typo

* include helpful stdout statements

* fix syntax; add helpful stdout

* Ensure files are written as GCP URIs

* add read files to export table

* Fix typo

* update output variable name

* Update README.md

* Update to gambit 0.4.0

* fix outputs

* correct if statement syntax

* remove apollo workflows from dockstore

* Remove apollo workflows

* Remove threshold outputs

* write predicted taxon/rank if next is none

* remove next taxon outputs

* add mycobacterium typing

* add tbprofiler params

* fix wdl syntax

* fix float

* add tbouts to export table

Co-authored-by: Michael Jared Lumpe <mjlumpe@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

Update version to v0.2