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Use groovy to parse samplesheets #243

Merged
merged 9 commits into from
Feb 15, 2024
Merged

Use groovy to parse samplesheets #243

merged 9 commits into from
Feb 15, 2024

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nebfield
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@nebfield nebfield commented Feb 15, 2024 •
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  • Deprecate samplesheet_to_json module
  • Set up groovy class to parse samplesheets
    • will automatically mount non-standard singularity directories (tested on CSC Puhti)
  • 🚨 json message structure has been updated 🚨 (samplesheet unaffected)

closes #240 #225

@nebfield nebfield changed the base branch from main to dev February 15, 2024 15:44
@nebfield nebfield changed the title Use groovy class to parse samplesheets Use groovy to parse samplesheets Feb 15, 2024
@nebfield nebfield mentioned this pull request Feb 15, 2024
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@nebfield nebfield marked this pull request as ready for review February 15, 2024 16:45
smlmbrt
smlmbrt approved these changes Feb 15, 2024
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Looks good, and seems like it solves 2 problems at once!

@nebfield nebfield merged commit cc163b7 into dev Feb 15, 2024
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@nebfield nebfield deleted the fix-mounts branch February 15, 2024 17:19
nebfield added a commit that referenced this pull request Mar 19, 2024
@nebfield @smlmbrt
v2.0.0-alpha.5 (#244)
538a01d 
* Update base.config

Match error-handling from nf-core (solves problem with status 140 that I had)

* Use groovy to parse samplesheets (#243)

* implement groovy functions for samplesheet parsing

* set up utility class

* add build to map

* add json support

* rename json parser

* delete samplesheet module

* remove mount docs (deprecated)

* remove out.json from expected test output

* fix parsing vcf samplesheet

* Update report (renv and include licenses) (#203)

* fix report link and setup renv lockfile

* update dockerfile to use renv

* add license terms

* clarify custom scores + licenses

* keep empty file in assets folder for optional input

* Drop aggregation during report generation (#249)

* drop small sampleset warning when integrating reference data

* drop aggregation

* update lockfile: drop data.table

* load scores the same way

* bump utils version

* drop effect_type (shouldn't actually be in columns array)

* use dev image

* update score test

* fix test

* bump pgscatalog_utils version

* boring but big: re-sync nf-core

* fix cache error in report

* nf-core resync

* set deno dir

* update schema

* set up auto-generated environment

* set workDir consistently

* improve caching

* fix help

* set outdir default

* use binary packages to build report image

* fix missing dependencies

* fix fraposa_pca

* add storeDir to relabel_ids

* fix score metadata in report

* store results permanently

* write to genotypes_cache, if set

* update conda

* add custom example scorefile

* Update schema to say what the cache is for

* Add information on cache and pipeline speed

* Not only for -resume

* fix storeDir

* fix tempdir on HPC/singularity

* gcp compatbility updates

* remove semantic structure from storeDirs (bad)

* Update cache.rst

* don't copy twice

* bump report singularity version

* fix quarto

* fix output

* fix fraposa

* fix capturing intersect counts

---------

Co-authored-by: smlmbrt <sam.a.lambert@gmail.com>

* Fix cache names (#260)

* Update plink2_makebed.nf

Remove chromosome so that it doesn't cause cache collision (should only run once per sampleset anyways)

* Fix prefix and output names

* Remove chromosome ID from orient

* set pytest version

* fix node deprecation warnings

* bump pytest-workflow

* downgrade pytest

* fix node deprecation warning

* bump python action again

* fix tmpdir errors in report

* fix --genotypes_cache

* make temporary dir in working directory

* fix missing cachedir

* cache relabelled afreq and variants separately

* oops

* add changelog to docs

* bump report from dev to production

* fix report distribution plots for non-ancestry runs

* Update arm.rst with new profile

* add deeep cache

* stop using wildcards

* swap cross operator -> combine

* set pgscatlaog_utils version to v0.5.2

* fix log output

* fix match_combine cache

* oops

* fix score aggregation cache

* error if scoring files don't get a calculation result

* update error strategy

* fix missing quarto package

* Fix race condition in cache (#262)

* stop using global variables

* use local variables

* Add information about versions

* add version to report (#265)

* add version to report

* update author

---------

Co-authored-by: Sam Lambert <sam.a.lambert@gmail.com>
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@nebfield @smlmbrt