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Merge branch 'dev' into unify_DE_params
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‎CHANGELOG.md‎

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### Changed
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- [[#676](https://github.com/nf-core/differentialabundance/pull/676)] - Derive differential result display columns at runtime instead of setting them in user-editable profiles. ([@antoniasaracco](https://github.com/antoniasaracco), review by [@pinin4fjords](https://github.com/pinin4fjords)).
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- [[#705](https://github.com/nf-core/differentialabundance/pull/705)] - Bump all modules and subworkflows to latest nf-core versions. Use Seqera containers in all modules. ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
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- [[#704](https://github.com/nf-core/differentialabundance/pull/704)] - Bump shinyngs modules to improve validation of contrasts and update subworkflows ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila), [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
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- [[#702](https://github.com/nf-core/differentialabundance/pull/702)] - Update limma and dream modules to put variable of interest first in zero intercept constrasts ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila), [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
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- [[#662](https://github.com/nf-core/differentialabundance/pull/662)] - Migrate to new workflow output format ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@grst](https://github.com/grst)).

‎modules.json‎

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"nf-core": {
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"affy/justrma": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "07cee52e08af8100eee4ea1b53abf0660df77701",
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"installed_by": ["modules"]
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},
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"atlasgeneannotationmanipulation/gtf2featureannotation": {
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"branch": "master",
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},
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"csvtk/join": {
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"git_sha": "945dd56498e7ec040c1cc0773860b9cc162cdc18",
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"installed_by": ["modules"]
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},
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"custom/filterdifferentialtable": {
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"branch": "master",
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"installed_by": ["abundance_differential_filter"]
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},
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"custom/matrixfilter": {
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"branch": "master",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"custom/tabulartogseachip": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "07cee52e08af8100eee4ea1b53abf0660df77701",
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"installed_by": ["differential_functional_enrichment"]
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},
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"custom/tabulartogseacls": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["differential_functional_enrichment"]
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},
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"custom/tabulartogseagct": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["differential_functional_enrichment"]
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},
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"decoupler/decoupler": {
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["differential_functional_enrichment"]
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},
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"deseq2/differential": {
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"branch": "master",
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"git_sha": "1db9cb151f557371e97a034dd7fadf1e60a15acd",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["abundance_differential_filter"]
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},
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"geoquery/getgeo": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "07cee52e08af8100eee4ea1b53abf0660df77701",
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"installed_by": ["modules"]
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},
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"gprofiler2/gost": {
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"branch": "master",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["differential_functional_enrichment"]
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},
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"gsea/gsea": {
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"branch": "master",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["differential_functional_enrichment"]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c",
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"installed_by": ["modules"]
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},
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"limma/differential": {
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"branch": "master",
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"git_sha": "07cee52e08af8100eee4ea1b53abf0660df77701",
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"installed_by": ["abundance_differential_filter", "modules"]
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},
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"propr/grea": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["differential_functional_enrichment"]
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},
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"propr/propd": {
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"branch": "master",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["abundance_differential_filter"]
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},
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"proteus/readproteingroups": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"]
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},
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"quartonotebook": {
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},
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"shinyngs/app": {
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"branch": "master",
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"git_sha": "f484e078bd49a19fceca5c54a09c585e518784c2",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"shinyngs/staticdifferential": {
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"branch": "master",
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"git_sha": "f484e078bd49a19fceca5c54a09c585e518784c2",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"shinyngs/staticexploratory": {
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"branch": "master",
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"git_sha": "f484e078bd49a19fceca5c54a09c585e518784c2",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"shinyngs/validatefomcomponents": {
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"branch": "master",
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"git_sha": "f484e078bd49a19fceca5c54a09c585e518784c2",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"untar": {
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"branch": "master",
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"git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"variancepartition/dream": {
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"branch": "master",
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"git_sha": "72348f04b265fb310f87db1c8d12e2151cbabe14",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["abundance_differential_filter", "modules"]
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},
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"zip": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"]
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"git_sha": "28cc100de441251ac7df8e7c65c63e9fd9557386",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/zip/zip.diff"
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}
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}
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},
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},
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"differential_functional_enrichment": {
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"branch": "master",
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"git_sha": "5d5b444114deab998a70bedf386f346d3ff2db51",
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"git_sha": "1bf1444fa67dc2934f6899a228a2e2034a0a354d",
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"installed_by": ["subworkflows"]
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"utils_nextflow_pipeline": {

‎modules/nf-core/affy/justrma/main.nf‎

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‎modules/nf-core/affy/justrma/meta.yml‎

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‎modules/nf-core/affy/justrma/tests/main.nf.test‎

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