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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

Commits on Apr 15, 2022

  1. New branch to get the pipeline to run again with the rnaseq changes

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  2. Added igenomes.config

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    WackerO committed Apr 15, 2022
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Commits on Apr 19, 2022

  1. Some changes

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  2. another save

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Commits on Apr 20, 2022

  1. seems to work, just need to figure out igenomes...

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  2. Seems to work know, however, I did not use params and instead just cr… 

    …eated the channels directly from the input/igenomes values in rnadeseq.nf
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Commits on Apr 21, 2022

  1. Updated Changelog and docu and added test profiles, also removed some… 

    … prints etc.
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  2. Removed a write command

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    WackerO committed Apr 21, 2022
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  3. Updated Changelog

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    WackerO committed Apr 21, 2022
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  4. Updated nextflow config and schema

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    WackerO committed Apr 21, 2022
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  5. Fixed some linting and prettier stuff

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    WackerO committed Apr 21, 2022
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  6. Further linting fixes

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    WackerO committed Apr 21, 2022
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  7. Added libs to env.yml

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Commits on Apr 28, 2022

  1. More cleaning up, the nextflow params problem is solved, added a star… 

    …_salmon test dataset in the testdata in a subfolder
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Commits on Apr 29, 2022

  1. Added rsem tests, replaced blacklist for pathway analysis with trycatch

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  2. Removed some more occurrences of blacklist

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  3. Fixed linting

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  4. Fixed usage.md format, update Changelog

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  5. Merge branch 'dev' into newseq2

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Commits on May 2, 2022

  1. Again removed the second redundant container definition in nextflow.c… 

    …onfig
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  2. Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne… 

    …wseq2
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  3. Removed unnecessary closing # at bottom of yml files

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  4. Removed another #

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Commits on May 3, 2022

  1. Merge branch 'dev' into newseq2

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    WackerO authored May 3, 2022
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  2. Made sample table sortable and searchable, but report title stuff is … 

    …broken now...
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  3. Fixed the broken title; that was because autoformat added two linebreaks

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    WackerO committed May 3, 2022
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  4. Removed blacklist parameter and test profile

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Commits on May 4, 2022

  1. Updated configs

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  2. Changed configs, changed internal parameter name counts to gene_counts

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  3. Changed internal parameter name counts -> gene_counts

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  4. Update modules/local/deseq2.nf 

    Co-authored-by: Gisela Gabernet <[email protected]>
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  5. Update bin/DESeq2.R 

    Co-authored-by: Gisela Gabernet <[email protected]>
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  6. Update bin/DESeq2.R 

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  7. Update bin/DESeq2.R 

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  8. Update bin/DESeq2.R 

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  9. Update bin/DESeq2.R 

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  10. Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne… 

    …wseq2
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  11. Changed flag name

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Commits on May 5, 2022

  1. Fixed some PR comments, species library version is now printed in rep… 

    …ort, added test datasets for newseq stuff
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  2. Auto-fixed linting_comment with nf-core lint

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  3. Merge branch 'newseq2' into iatable

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  4. Added logFCthreshold = 2 to some more test configs, renamed two test … 

    …configs
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  5. Update bin/DESeq2.R 

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Commits on May 6, 2022

  1. Update bin/DESeq2.R 

    Co-authored-by: Gisela Gabernet <[email protected]>
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  2. Update bin/DESeq2.R 

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  3. Update bin/DESeq2.R 

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  4. Applied some suggested changes to DESeq2.R, removed save copies of te… 

    …stdata
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  5. Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne… 

    …wseq2
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  6. Applied further suggestions

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  7. Fixed some errors, changed some remaining rawcounts to featurecounts

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  8. Fixed space

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  9. Uploaded test datasets

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  10. Changed ci.yml for the new tests

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Commits on May 9, 2022

  1. Removed comment

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  2. Update bin/pathway_analysis.R 

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  3. Update docs/usage.md 

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  4. Update docs/usage.md 

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  5. Update docs/usage.md 

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  6. Update nextflow.config 

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  7. Applied some suggestions

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  8. Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne… 

    …wseq2
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  9. Added a comment

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  10. Update nextflow_schema.json 

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Commits on May 11, 2022

  1. Removed Lab ID from the report

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  2. Merge branch 'newseq2' of https://github.com/WackerO/rnadeseq into ne… 

    …wseq2
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  3. Changed Schema groovy to match template

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  4. Merge branch 'newseq2' into iatable

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  5. Added comment

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  6. Merge branch 'newseq2' into iatable

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  7. Updated changelog

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  8. Switched some more = for ~

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  9. tMerge branch 'newseq2' into iatable

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