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Interactive report tables #122

Merged
merged 72 commits into from
May 11, 2022
Merged

Interactive report tables #122

merged 72 commits into from
May 11, 2022

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WackerO
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@WackerO WackerO commented May 11, 2022

Many thanks to contributing to qbic-pipelines!

This PR introduces interactive tables in the report that can be searched and sorted. Please merge before export.

PR checklist

  • This comment contains a description of changes (with reason)
  • [] If you've fixed a bug or added code that should be tested, add tests!
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: https://github.com/qbic-pipelines/rnadeseq/tree/master/.github/CONTRIBUTING.md

WackerO and others added 30 commits April 15, 2022 19:55
@WackerO
New branch to get the pipeline to run again with the rnaseq changes
f59696e
@WackerO
Added igenomes.config
f9741c1
@WackerO
Some changes
6fe9e09
@WackerO
another save
869246f
@WackerO
seems to work, just need to figure out igenomes...
e7180c1
@WackerO
Seems to work know, however, I did not use params and instead just cr…
eeaae6a 
…eated the channels directly from the input/igenomes values in rnadeseq.nf
@WackerO
Updated Changelog and docu and added test profiles, also removed some…
4fffb90 
… prints etc.
@WackerO
Removed a write command
f4dd6f8
@WackerO
Updated Changelog
4c95a03
@WackerO
Updated nextflow config and schema
a170317
@WackerO
Fixed some linting and prettier stuff
029511c
@WackerO
Further linting fixes
8d6904c
@WackerO
Added libs to env.yml
7e0b849
@WackerO
More cleaning up, the nextflow params problem is solved, added a star…
9fcec59 
…_salmon test dataset in the testdata in a subfolder
@WackerO
Added rsem tests, replaced blacklist for pathway analysis with trycatch
2552dd6
@WackerO
Removed some more occurrences of blacklist
934f0de
@WackerO
Fixed linting
93378e9
@WackerO
Fixed usage.md format, update Changelog
0ee6911
@WackerO
Merge branch 'dev' into newseq2
5430974
@WackerO
Again removed the second redundant container definition in nextflow.c…
7fdb229 
…onfig
@WackerO
Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne…
b6dee97 
…wseq2
@WackerO
Removed unnecessary closing # at bottom of yml files
fc86b90
@WackerO
Removed another #
65e39c8
@WackerO
Merge branch 'dev' into newseq2
a007576
@WackerO
Made sample table sortable and searchable, but report title stuff is …
fea9ba2 
…broken now...
@WackerO
Fixed the broken title; that was because autoformat added two linebreaks
0777736
@WackerO
Removed blacklist parameter and test profile
32ef43f
@WackerO
Updated configs
15e6cd8
@WackerO
Changed configs, changed internal parameter name counts to gene_counts
2d3f354
@WackerO
Changed internal parameter name counts -> gene_counts
4e709ef
WackerO and others added 24 commits May 6, 2022 08:49
@WackerO
Applied some suggested changes to DESeq2.R, removed save copies of te…
8f73145 
…stdata
@WackerO
Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne…
a7d7ea5 
…wseq2
@WackerO
Applied further suggestions
3562d94
@WackerO
Fixed some errors, changed some remaining rawcounts to featurecounts
a4113f0
@WackerO
Fixed space
aa58784
@WackerO
Uploaded test datasets
628775c
@WackerO
Changed ci.yml for the new tests
6b505f1
@WackerO
Removed comment
815fc8f
@WackerO @ggabernet
Update bin/pathway_analysis.R
f5109fc 
Co-authored-by: Gisela Gabernet <[email protected]>
@WackerO @ggabernet
Update docs/usage.md
55e58e5 
Co-authored-by: Gisela Gabernet <[email protected]>
@WackerO @ggabernet
Update docs/usage.md
f73f8c7 
Co-authored-by: Gisela Gabernet <[email protected]>
@WackerO @ggabernet
Update docs/usage.md
8590319 
Co-authored-by: Gisela Gabernet <[email protected]>
@WackerO @ggabernet
Update nextflow.config
ecbe993 
Co-authored-by: Gisela Gabernet <[email protected]>
@WackerO
Applied some suggestions
e6579d8
@WackerO
Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne…
d1ca507 
…wseq2
@WackerO
Added a comment
811b103
@WackerO @ggabernet
Update nextflow_schema.json
d29c58a 
Co-authored-by: Gisela Gabernet <[email protected]>
@WackerO
Removed Lab ID from the report
8a42bbd
@WackerO
Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne…
756469c 
…wseq2
@WackerO
Changed Schema groovy to match template
e05b9a1
@WackerO
Merge branch 'newseq2' into iatable
e1e0381
@WackerO
Added comment
5b07577
@WackerO
Merge branch 'newseq2' into iatable
7b9fde3
@WackerO
Updated changelog
d4e1e9d
@WackerO WackerO requested a review from ggabernet May 11, 2022 12:44
ggabernet
ggabernet approved these changes May 11, 2022
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Looks good to me

@WackerO WackerO merged commit d58f8c4 into qbic-pipelines:dev May 11, 2022
@WackerO WackerO deleted the iatable branch July 27, 2022 09:00
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@ggabernet ggabernet ggabernet approved these changes

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@WackerO @ggabernet