[BIG] Adding spoQC to spatialaxe and many other changes - #206

Merged

heylf merged 76 commits into

nf-core:devfrom

Aug 18, 2026

Commits on Jul 23, 2026

adding spoqc to spatialaxe
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5f6b97a
changing spatialdata_wrote.py
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40bef22

Commits on Jul 27, 2026

all tests pass now for spoQC
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bab69c8
updating nextflow configs for the analysis modules
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3254152
update README
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603637d

Commits on Jul 31, 2026

adding new module of the final report of spoQC and little changes to other spoQC modules
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1112d71

Commits on Aug 6, 2026

change to final_report main.nf and meta.yml
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374a9b6

Commits on Aug 7, 2026

adding unzip to pipeline for a bigger test data set
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ac3a289
changes to lots tests for spoqc modules main.nf.test
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62ccb66
adding bigger test data samplesheet_full.csv, test_full.config and main.nf for utils_nfcore_spatialaxe
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c5b9e64
add untzip to spatialaxe.nf
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927aa6e
add test config for spoqc subworkflow
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5a41ec8
adding spoqc test, change to .nfignore and spoqc.nf.test and spoqc.nf.test.snap
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f653407
change to snapshot for final_report main.nf.test.snap
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7e5f020
Merge branch 'spoqc' into dev
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48339a9
Merge pull request #4 from heylf/dev
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a6dfffc
change to ro-create-metadata.json
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a933a14
change to nextflow_schmea.json
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dcea0c6
apply prettier modules.json
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08217a4
changes to modules.json
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d1d824a
changes to nextflow_schmea.json
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9862dc0
update nextflow schmema to 2.7.2
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73d3207
update subworkflow/nf-core/ultis_nextflow_pipeline
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7b88bdd
tiny change to modules.config
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bb1dba8
simplify for spoqc the modules.config
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32ffd20
change to spoqc resources
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55d48d9
add combinatorial cpu labels to base.config
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0de40f4
add combinatorial cpu labels to spoqc modules
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3df9d01
bugfix because of new nf-core schema version
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1bc8bf7
remove spatialdata write from spoqc subworkflow, hcange ot main.nf
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65ff8f2
allow for qc mode only approach, change to spatialdata_write_meta_ermge subworkloe, change to mainf and spatialaxe.nf
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84fbfb6
add all changes to CHANGELOG.md
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bb74a0c
fix in CHANGELOG.md
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9236b5f
change to CHANGELOG.md
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ccca85e
update to usage.md
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dfecd6e
add spoqc to output.md
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5b52705
change to module.jon
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f9ec855
trim white spaces
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6ff22fd
end-of-file-fixer
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4a14fc1
end-of-file-fixer
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53312b9
update nextflow version
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8a131f5
update nextflow version
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246d2cd
upating snapshots
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14a6a10

Commits on Aug 11, 2026

update tests and snaps for spoqc modules
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b773d8a
add MIT license to met.ymls
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21bec3a
change to modules.config
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879940a
change to spoqc modules main.nf
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8c11bee
change to spatialaxe.nf
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011e6d0
changes to spoqc meta.ymls
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3e7f478
change to spoqc module meta.ymsl
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f575073
change spoq subwofklow main.nf, spatialaxe.nf and hqpr_metircs/main.nf
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5485462
change to spoqc subworkflow main.nf and meta.yml
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2b5c0a2
change id name for sampleshee_full.csv
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44d6865

Commits on Aug 12, 2026

bug fixes for spoqc subworkflow main.nf
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d199c64
change to spoqc meta.ymls
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c807a2b
starting to add more QC readme stuff
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0dcb656
change description in all spoqc meta.ymls
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be8c67d

Commits on Aug 13, 2026

update to test and snapshots
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bf52082
solve the issue of template disagreement, change to output.md and README.md
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7a67920
change to qc.md
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a2e71af
trim white space spoqc subworkflow main.nf
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2ffb212
change number of cpus in spoqc test nextflow.configs
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9aaca2f
same for spoqc subworfklow test configs
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f76936a
change memory for some spoqcm odules tests nextflow.configs
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15d8b44
change memory for some spoqcm odules tests nextflow.configs
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2c0d63b
changes to spoqc nf.test and nf.test.snap
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d1abbd3
update spoqc subworkflow snapshot
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807add1
change to coordinate_mode.nf.test.snap
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e62d7a7

Commits on Aug 14, 2026

bugfix for run_qc parameter. Implementing new test in coordinate_mode to acocunt for it cahgnes to subworkflow/spatialdata/main.nf, coordinat_mode.nf.test*, spatialaxe.nf
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c1ef0cb
update snaps
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15e02d2
update tests
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904d1df
update tests
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5c6bf9d
change .nftignore
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590e59a
update tests
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7f71d49
update tests
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f9241fc

Commits on Aug 15, 2026

update tests
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c5170af