fmalmeida
commented
2 years ago Before merging:
- [x] Update the .md files about the new version
Closed fmalmeida closed 2 years ago
fmalmeida
commented
2 years ago Before merging:
Split out the config profiles (#43)
Split out the config profiles
Resolve the conflict using the upstream config
trying to have a create dbs process
found way to download dbs
adding resfinder and plasmidfinder download rules
added phigaro, vfdb and amrfinder download rules
added last database download rules
added prokka HMM download rule
added label to use docker for tools
fixed argminer download
fixed victors download
fixed iceberg download
prokka using given database and bioconda image
docker specific for downloading databases
update packages
added mlst database download rule
add bacannot db info
also downloads PGAP db
added prokka and mlst
fix conditional
fixed pgap conditional
added barrnap
added 'compute_gc' module -- think about modules with two tools
adding identation
fixing label
first tries on conda envs
removing label
adding plasmidfinder
added platon
working until islandpath
added: VFDB
added: Victors
changing name and organization of MISC image
added: PHAST
added: phigaro
added: phispy
added: iceberg
added: kofamscan db download
removing named outputs as it will be solved in another PR
added: kofamscan from downloaded database
added: kegg_decoder
Refactor channel identifiers and process names (#45)
Main change
Processes, channels and workflow names have had its case names changed in order to meet nextflow's community standards.
Commits
Co-authored-by: Felipe Marques de Almeida felipemarques89@gmail.com
trying to brind amrfinder, card_rgi and argminer
trying to fix how the scale is calculated for amrfinder
changing scale to perl
typo fix
removing unnecessary comma
Update amrfinder.nf
passing calculation of thresold into two decimals scale to groovy
properly working until amrfinder and card_rgi
added small dataset test profile
fixing name of quicktest profile
fixing urls of testing samplesheets
removing unnecessary files
fix missing label
adding resfinder to miscellaneous image
fixing gitignore
change manifest to upcoming version
updating db download workflow behaviour
removing .git dirs
fixing argminder download
properly added resfinder
adding script that parses nanopolish methyl call
removing unnecessary labels
starting to change how images are done
added perl tools
Added:
prokka
barrnap
mlst
added misc module
added:
gc_compute module
adding labels
added kofam analysis
added main pyenv
added tools:
platon
plasmidfinder
fixed perlenv image
Added tool:
islandpath
included virulence modules
they use the miscellaneous image
added prophage tools:
phast scan
phigaro *phispy
added iceberg db module
it uses the miscellaneous image
added tool:
rgi
added resistance tools
added:
argminer db module
resfinder
amrfinderplus
added nanopolish
added refseq_masher
added digIS
Docker image and modules were updated to run until digIS
added antismash
added sequence server
added merge_annotation module
added draw_gis modules
added gff2gbk module
added create_sql module
added first resource management labels
fixing resouce label for phigaro
little finx in env
fixing how tuples should be passed
arrived at jbrowse step
fixing draw_gis module input tuple
jbrowse added
Create test_pr.yml
This is how new versions will be organised after the remodeling branch update, and, therefore, the test_pr must be updated.
fixed phast db incorporation
fixing inputs on report
Update test_pr.yml
Will only act in ready for review PRs
adding ENV VAR for current version
adding scripts to automatically build images
fixed iceberg db incorporation
Update digIS.nf
DIGis gff usage fixed
fixed vfdb incorporation
changing file to path input resolution
fixed victors db incorporation
changed channel names in main script
fixed argminer and prokka tables
fixed custom db annotations incorporation
fixed bacannot server loading
fixed custom db reports
begin incorporation of nf-core framework
nf-core libs have been added to the pipeline
custom database annotation added to JBrowse
fixed custom database gff generation
Update Dockerfile
diminished image size by removing antismash db from inside it
uncommenting assemblers images
creating singularity profile
begin documentation update
added singularity profile
made image compatible with earlier versions
given 777 permissions to workdir
adjusted default values
fixed prokka to work with singularity
fixed rgi for singularity usage
updating PR test action
update targeted branches
limiting process resources
updated image for singularity
removing unused dbs in quicktest
not using big dbs in quicktest
Update resfinder.nf
adding gitpod config
fixed yml
fixing custom db report getattributefileld snippet
begin change to mkdocs
add requirements
Update .readthedocs.yml
Update .readthedocs.yml
Update .readthedocs.yml
Update .readthedocs.yml
update
update requirements
added index
fixed tags
added installation information
now on quickstart
changed some admonitions
added quickstart
added samplesheet page to mkdocs
included dir with images
Update samplesheet.md
fixed header levels
outputs page added to mkdocs
Update standard.config
removing "paralallel_jobs" definition
fixed blast default values
updated and tested quickstart
updating gitpod.yml
creates a testing dir with more space
added profile selection information
Update manual.md
manual updated for mkdocs and with new --ncbi_proteins parameter
updated --custom_db parameter description
removed parameters that are in default and should not be in the boilerplate
added config file page
information about custom databases added
Update nextflow_schema.json
defaults need to be loaded before boilerplate
changing label of unicycler and flye
fixed antismash installation
fixed keggdecoder requires py36
fixed resfinder module
fixed db setup
Co-authored-by: Abhinav Sharma abhi18av@users.noreply.github.com