Pipeline remodelling. Issues 24, 31 and 36 (#44)

[fmalmeida]

• Split out the config profiles (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 (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

• Refactor names
• refactor names in the workflows
• Update workflows/bacannot.nf
• Update workflows/bacannot.nf
• Apply suggestions from code review
• Update workflows/bacannot.nf wrt iceberg
• Accomodate code review and fix the channel name
• fix MERGE_ANNOTATIONS process case in line 331

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

• pyenv image updated

added prophage tools:

• phast scan

• phigaro
  *phispy

• added iceberg db module

it uses the miscellaneous image

• added py36env 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

• Update docker.config

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

• Update defaults.config

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

• Update nextflow_schema.json

updated --custom_db parameter description

• Update nextflow.config

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

• pipeline fixed for docker

Co-authored-by: Abhinav Sharma abhi18av@users.noreply.github.com

[fmalmeida]

Before merging:

• Update the .md files about the new version