What’s Changed

• Add PGEcore as a submodule by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/1
• Feature/add count samples by coi module by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/4
• Update PGEcore by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/6
• Adding dockerfile by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/5
• Updating Dockerfile for more R packages by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/10
• Feature/extract allele table by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/7
• Update pg ecore by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/18
• Feature/idm module by @a-hubbard in https://github.com/nf-core/plasmodiumdrugres/pull/15
• Feature/allele prev naive by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/13
• updated docker and PGEcore to remove devtools dependency; by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/21
• Feature/translate loci of interest by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/11
• adding pileup_specific_snps; by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/17
• Add module and tests for slaf_from_stave_mlaf.R by @a-hubbard in https://github.com/nf-core/plasmodiumdrugres/pull/19
• Rename IDM module emission from slaf_output to slaf by @a-hubbard in https://github.com/nf-core/plasmodiumdrugres/pull/22
• Feature/naive coi by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/16
• Rename IDM_wrapper.nf to idm_wrapper.nf by @a-hubbard in https://github.com/nf-core/plasmodiumdrugres/pull/25
• Update column names in allele table by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/26
• Feature/multilocus prev freq naive by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/24
• Feature/mlbm module by @a-hubbard in https://github.com/nf-core/plasmodiumdrugres/pull/23
• Feature/add allele freq naive by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/27
• fix md5sum check for mlbm by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/29
• added nextflow for extract ref_seqs via fasta or a genome; by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/28
• Feature/extract panel to bed by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/31
• Updating Dockerfile and PGEcore by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/33
• Feature/dcifer module by @a-hubbard in https://github.com/nf-core/plasmodiumdrugres/pull/30
• update PGEcore; update mlaf for new PGEcore function; updated md5sum … by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/35
• exposed a new MLBM argument for filtering low occurrence aa calls; by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/42
• Updating main drug resistance pipeline by @nickjhathaway in https://github.com/nf-core/plasmodiumdrugres/pull/44
• Feature/add main drug res workflow by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/39
• Feature/update pgecore version by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/47
• Hotfix/update aa table split by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/48
• Hotfix/update default methods by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/49
• Feature/generate population map from pmo by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/50
• update docs by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/51
• Feature/dockerhub deploy by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/53
• update author to PlasmoGenEpi for dockerfile by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/54
• Dev by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/55
• add instructions about cloning the repo by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/60
• Hotfix/add temporary nextflow note by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/66
• add instructions for pulling image with different platform and remove… by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/65
• Hotfix/docker failing build by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/71
• Update colours, tools, and structure of metro map by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/70
• Stop tracking .vscode and ignore i by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/74
• index population assignment and use this internally to remove issues … by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/73
• Hotfix/update test data by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/79
• update linting param intput by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/77
• Update to use the nf-core test repo data by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/80
• Feature/create conda environments by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/81
• Update syntax for nextflow 26 by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/82
• Template sync by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/84
• Update tool option handling and add subworkflow meta files by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/85
• Standardise outputs from tools by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/75
• allow no loci groups and ml won’t run by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/78
• Accurately represent current state in metromap; Update colours by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/88
• Hotfix/update env documentation by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/89
• bump pipeline version for release and update snapshots by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/86
• Add manifest.diagram to nextflow.config by @ewels in https://github.com/nf-core/plasmodiumdrugres/pull/91
• Update pipeline to use new PGEcore R package by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/92
• Add date to change log; remove nf-core todo from conributing doc by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/93
• Add fem coi as a parameter that can be passed to the pipeline by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/95
• Hotfix/unnasigned specimens by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/94
• Use real surveillance data for test_full; set collapse to full; colla… by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/103
• Add white panel to metromap for darkmode by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/105
• Hotfix/tidy docs and modules by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/107
• Switch fix-linting to the hardened nf-core/actions reusable workflow by @mashehu in https://github.com/nf-core/plasmodiumdrugres/pull/111
• Hotfix/release blockers by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/112
• Update default branch to main by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/96
• Update date of release by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/114
• Dev by @kathrynmurie in https://github.com/nf-core/plasmodiumdrugres/pull/90

New Contributors

• @kathrynmurie made their first contribution in https://github.com/nf-core/plasmodiumdrugres/pull/1
• @nickjhathaway made their first contribution in https://github.com/nf-core/plasmodiumdrugres/pull/10
• @a-hubbard made their first contribution in https://github.com/nf-core/plasmodiumdrugres/pull/15
• @ewels made their first contribution in https://github.com/nf-core/plasmodiumdrugres/pull/91
• @mashehu made their first contribution in https://github.com/nf-core/plasmodiumdrugres/pull/111

Full Changelog: https://github.com/nf-core/plasmodiumdrugres/commits/1.0.0