v1.0.0-alpha: Iterating for publication work

Full Changelog: v0.9.9...v1.0.0-alpha

1. Refactor the NORMAL_MODE to simply be the default mode

2. Improve the test profiles

v0.9.9: Finishing touches for the publication

What's Changed

• Add multiqc report by @Mxrcon in #87
• Add library parameter to samplesheet by @Mxrcon in #88

Full Changelog: v0.9.8...v0.9.9

v0.9.8: Transition to nf-core template

What's Changed

• Use nf-core template for the pipeline to facilitate standardisation by @abhi18av in #84
• [PATCH] Using biocontainers and removing custom container version by @Mxrcon in #85
• Modifications after extensively iterations on Virtual Machine by @Mxrcon in #86

Full Changelog: v0.9.7...v0.9.8

v0.9.7: Test release for clusters

What's Changed

• Bundle the gatk jar in the container by @abhi18av in #75

Full Changelog: v0.9.6...v0.9.7

v0.9.6: Inching towards v1.0

Full Changelog: v0.9.5...v0.9.6

v0.9.5: Redesign the UX for the pipeline

What's Changed

• Updating the documentation for MEDTROP presentation by @Mxrcon in #73
• Improvements to the design and defaults by @abhi18av in #74

Full Changelog: v0.9.4...v0.9.5

Fix QC flow

What's Changed

• [Fix] Preventing workflows from caching the samples.tsv for cohort steps by @Mxrcon in #66
• [FIX] Found errors in qc after debbuging by @Mxrcon in #69

Full Changelog: v0.9.3...v0.9.4

v0.9.3: Testing done on cloud/server/cluster

What's Changed

• Add reference files for MTB by @emilyncosta in #49
• [DEV] Adding a channel for references by @Mxrcon in #48
• Release 0.9.3 by @emilyncosta in #50
• [DEV ] Adding a qc report report workflow by @Mxrcon in #56
• [MAINTENANCE] Adding a test workflow and updating the Makefile by @Mxrcon in #61
• [FIX] Adding specific tag to conda recipe by @Mxrcon in #64

New Contributors

• @emilyncosta made their first contribution in #49

Full Changelog: v0.9.2...v0.9.3

Global config file for all mtbseqs and nextflow params

Release 0.9.2 (#43)

* add nextflow schema

* remove hidden fields

* tweak the schema

* format files using intellij

* [FIX] Syncing stubs and scripts (#38)

* Add a basic nextflow_schema file (#37)

* add nextflow schema

* remove hidden fields

* tweak the schema

* fixing all stubs as requested

* adding stubs to rename_files module

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

* update readme and trim config

* update the readme

* tweak readme

* Further updates for the readme

* update readme

* updated the benefits for NF wrapper

* [DEV] adding dag resources (#41)

* adding dag as png

* adding a topic to readme

* fixing wrong format

* fixing `dag-batch.png`

* Update error strategy (#42)

* Stubs and DAG file (#39)

* add nextflow schema

* remove hidden fields

* tweak the schema

* format files using intellij

* [FIX] Syncing stubs and scripts (#38)

* Add a basic nextflow_schema file (#37)

* add nextflow schema

* remove hidden fields

* tweak the schema

* fixing all stubs as requested

* adding stubs to rename_files module

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

* update readme and trim config

* update the readme

* tweak readme

* Further updates for the readme

* update readme

* updated the benefits for NF wrapper

* [DEV] adding dag resources (#41)

* adding dag as png

* adding a topic to readme

* fixing wrong format

* fixing `dag-batch.png`

Co-authored-by: Davi Marcon <48180517+Mxrcon@users.noreply.github.com>

* Update standard.config

Co-authored-by: Davi Marcon <48180517+Mxrcon@users.noreply.github.com>

* ready for review

* [DEV] Adding notes about the native commands  (#44)

* adding my org notes

* removing org file and adding a markdown file

* restructure order of config values

Co-authored-by: Davi Marcon <48180517+Mxrcon@users.noreply.github.com>

Functional code and DAGs

Stubs and DAG file (#39)

* add nextflow schema

* remove hidden fields

* tweak the schema

* format files using intellij

* [FIX] Syncing stubs and scripts (#38)

* Add a basic nextflow_schema file (#37)

* add nextflow schema

* remove hidden fields

* tweak the schema

* fixing all stubs as requested

* adding stubs to rename_files module

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

* update readme and trim config

* update the readme

* tweak readme

* Further updates for the readme

* update readme

* updated the benefits for NF wrapper

* [DEV] adding dag resources (#41)

* adding dag as png

* adding a topic to readme

* fixing wrong format

* fixing `dag-batch.png`

Co-authored-by: Davi Marcon <48180517+Mxrcon@users.noreply.github.com>