Comorment-Containers-v1.9.0 (COSGAP)

This is a major update with a number of changes since 1.8.1 (see below).
Notably, the project is referred to as COSGAP (COntainerized Statistical Genetics Analysis Pipelines) as described in our paper, and container builds are now removed from the git history and are available from ghcr.io as described in the installation procedures.

What's Changed

• Revised autodocs build by @espenhgn in #231
• Updated LDpred2 examples by @deepchocolate in #233
• Deprecate Saige by @ttfiliz in #239
• Documentation updates by @espenhgn in #240
• references by @espenhgn in #242
• citation stuff by @espenhgn in #243
• add --extract and --exclude options to filter snps in gwas.py by @ttfiliz in #244
• r.sif: Rstudio-server docs by @espenhgn in #248
• gwas.sif: build regenie with HAS_BOOST_IOSTREAM=1 by @espenhgn in #250
• Build container image hello:latest using build action by @espenhgn in #252
• Revert "Build container image hello:latest using build action " by @espenhgn in #253
• Update run_ldpred2_slurm.job by @espenhgn in #254
• add support for additional options in gwas.py by @ttfiliz in #246
• Add container build/push actions by @espenhgn in #260
• Fixed wrong Docker build target by @espenhgn in #262
• search and replace r fix by @espenhgn in #264
• Update gSEM Git SHA by @juuf in #265
• bump wget version by @espenhgn in #266
• fix GLIBCXX_3.4.30 not found; conda env; fix broken tests by @espenhgn in #268
• buggered ldak download by @espenhgn in #272
• python3: add missing packages by @espenhgn in #274
• Run unit tests during Docker build procedure by @espenhgn in #277
• Fix broken build-push action by @espenhgn in #279
• Missing tools/packages to Python3/R containers by @espenhgn in #281
• bump fossil version by @espenhgn in #282
• Containerize missing tools/update by @espenhgn in #289
• Build-push actions fail: oras: not found by @espenhgn in #291
• LDpred2: Add --file-drop-snps argument by @espenhgn in #293
• Containerize tools by @espenhgn in #295
• structure for singularity/containers directory by @espenhgn in #296
• updated changelog for 1.9.0 by @espenhgn in #298

New Contributors

• @juuf made their first contribution in #265

Full Changelog: v1.8.1...v1.9.0

Comorment-Containers-v1.8.1

This is 1st bugfix release of the CoMorMent-Containers project since v1.8.0 release.
Confer also the CHANGELOG for an overview of changes since the v1.8.0 release

What's Changed

• Minor changes to documentation + suggestion of TOC by @ofrei in #228
• gwas.py: fixed gwas demo run and IID column position by @ttfiliz in #234

Full Changelog: v1.8.0...v1.8.1

CoMorMent-Containers-v1.8.0

This is 1st feature release of the CoMorMent-Containers project since v1.7.1 release.
Confer also the CHANGELOG for an overview of changes since the v1.7.1 release

What's Changed

• r.sif: Add CC-GWAS R package by @espenhgn in #226
• calculateLD.R: Fixed incorrect SNP map by @deepchocolate in #178

Full Changelog: v1.7.1...v1.8.0

CoMorMent-Containers-v1.7.1

Comorment-Containers-v1.7.1 Latest

This is 1st bugfix release of the CoMorMent-Containers project since v1.7.0 release.
Confer also the CHANGELOG for an overview of changes since the v1.7.0 release

What's Changed

• ldpred2.R: fix hg_38 should be hg38 and hg_18 should be hg18 by @espenhgn in #224

Full Changelog: v1.7.0...v1.7.1

Comorment-Containers-v1.7.0

This is 1st feature release of the CoMorMent-Containers project since v1.6.0 release.
Confer also the CHANGELOG for an overview of changes since the v1.6.0 release

What's Changed

• gwas.sif: Add samtools, bedtools, liftOver, upgrade others by @espenhgn in #222

Full Changelog: v1.6.0...v1.7.0

Comorment-Containers-v1.6.0

This is 1st feature release of the CoMorMent-Containers project since v1.5.1 release.
Confer also the CHANGELOG for an overview of changes since the v1.5.1 release

What's Changed

• Add/update requested gwas.sif binaries by @espenhgn in #214

Full Changelog: v1.5.1...v1.6.0

Comorment-Containers-v1.5.1

This is 1st bugfix release of the CoMorMent-Containers project since v1.5.0 release.
Confer also the CHANGELOG for an overview of changes since the v1.5.0 release

What's Changed

• Docs builds are failing on readthedocs.io by @espenhgn in #208

Full Changelog: v1.5.0...v1.5.1

CoMorMent-Containers-v1.5.0

This is 1st feature release of the CoMorMent-Containers project since v1.4.0 release.
Confer also the CHANGELOG for an overview of changes since the v1.4.0 release

What's Changed

• Add PRS tools by @espenhgn in #107

Full Changelog: v1.4.0...v1.5.0

CoMorMent-Containers-v1.4.0

This is 10th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• Fixed failed installation of minimac4 in gwas.sif by @espenhgn in #196

Full Changelog: v1.3.0...v1.4.0

CoMorMent-Containers-v1.3.9

This is 9th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• LDpred2.R: redirect temporary data during runs by @espenhgn in #204

Full Changelog: v1.3.0...v1.3.9