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Soft matrix support #136

Merged
merged 77 commits into from
Sep 12, 2023
Merged

Soft matrix support #136

merged 77 commits into from
Sep 12, 2023

Commits on Jun 13, 2023

  1. R script read from soft matrix

    Azedine Zoufir committed Jun 13, 2023
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  2. add read_from_soft process to pipeline

    Azedine Zoufir committed Jun 13, 2023
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  3. add configuration for read_from_soft process

    Azedine Zoufir committed Jun 13, 2023
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  4. incorporate read from soft process into workflow

    Azedine Zoufir committed Jun 13, 2023
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  5. add querygse as an input parameter to workflow

    Azedine Zoufir committed Jun 13, 2023
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  6. add querygse to schema

    Azedine Zoufir committed Jun 13, 2023
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  7. add 'non_affy_array' as possible value for study type param

    Azedine Zoufir committed Jun 13, 2023
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Commits on Jun 14, 2023

  1. fixing configs for read_from_soft process

    Azedine Zoufir committed Jun 14, 2023
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  2. fix geoquery container url in read_from_soft.nf

    Azedine Zoufir committed Jun 14, 2023
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  3. remove raw matrix processing for [non_affy_array] track

    Azedine Zoufir committed Jun 14, 2023
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  4. remove raw matrix processing for [non_affy_array] track

    Azedine Zoufir committed Jun 14, 2023
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  5. attempt to fix premature completion of pipeline

    Azedine Zoufir committed Jun 14, 2023
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  6. attempt to fix premature completion of pipeline

    Azedine Zoufir committed Jun 14, 2023
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  7. debug around contrasts & matrix filter

    Azedine Zoufir committed Jun 14, 2023
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  8. debug around contrasts & matrix filter

    Azedine Zoufir committed Jun 14, 2023
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  9. debug matrix input processing for exploratory plots in [non_affy_arra… 

    …y] track
    Azedine Zoufir committed Jun 14, 2023
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  10. do not filter matrix in [non_affy_array] track

    Azedine Zoufir committed Jun 14, 2023
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Commits on Jun 15, 2023

  1. revert debug and apply log2 transformation to READ_FROM_SOFT output

    Azedine Zoufir committed Jun 15, 2023
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  2. add test SOFT matrix track config

    Azedine Zoufir committed Jun 15, 2023
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  3. add test SOFT matrix track config

    Azedine Zoufir committed Jun 15, 2023
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  4. fix typo in config file

    Azedine Zoufir committed Jun 15, 2023
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  5. add extra input to READ_SOFT_MATRIX to process metacolumns (differ by… 

    … array platform)
    Azedine Zoufir committed Jun 15, 2023
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  6. fix typo in config

    Azedine Zoufir committed Jun 15, 2023
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  7. fix typo in config

    Azedine Zoufir committed Jun 15, 2023
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  8. fix parameter name in read_soft_matrix

    Azedine Zoufir committed Jun 15, 2023
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  9. fix parameter name in read_soft_matrix

    Azedine Zoufir committed Jun 15, 2023
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  10. change column names to GSM ids in configuration, to match SOFT format

    Azedine Zoufir committed Jun 15, 2023
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  11. update docs

    Azedine Zoufir committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. update docs

    Azedine Zoufir committed Jun 16, 2023
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  2. NA treatment when determining if log transformation needs to be applied

    Azedine Zoufir committed Jun 16, 2023
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  3. NA treatment when determining if log transformation needs to be applied

    Azedine Zoufir committed Jun 16, 2023
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Commits on Jun 28, 2023

  1. fix typo in test prior to differential process

    Azedine Zoufir committed Jun 28, 2023
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  2. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Jun 28, 2023
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Commits on Jun 30, 2023

  1. put changes back into v1.3.0

    Azedine Zoufir committed Jun 30, 2023
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  2. Merge branch 'soft_matrix_support' of https://github.com/nf-core/diff… 

    …erentialabundance into soft_matrix_support

merge
    Azedine Zoufir committed Jun 30, 2023
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  3. replace new study type [non_affy_array] by [geo_soft_file]

    Azedine Zoufir committed Jun 30, 2023
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  4. remove [querygse] and [features_metadata_cols] as input to read_soft … 

    …modules and use as params instead
    Azedine Zoufir committed Jun 30, 2023
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  5. Merge branch 'dev' into soft_matrix_support

    @azedinez
    azedinez committed Jun 30, 2023
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  6. fix linting/indents in read_soft_matrix.R

    Azedine Zoufir committed Jun 30, 2023
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  7. Merge branch 'soft_matrix_support' of https://github.com/nf-core/diff… 

    …erentialabundance into soft_matrix_support
    Azedine Zoufir committed Jun 30, 2023
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  8. remove usage of 'non affymetrix' in docs and stress that's is a diffe… 

    …rent use case
    Azedine Zoufir committed Jun 30, 2023
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  9. name input channel for soft rather than generic

    Azedine Zoufir committed Jun 30, 2023
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  10. handle features from soft separately from user provided features 

    Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
    @azedinez @pinin4fjords
    azedinez and pinin4fjords committed Jun 30, 2023
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  11. handle features from soft separately from user provided features 

    Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
    @azedinez @pinin4fjords
    azedinez and pinin4fjords committed Jun 30, 2023
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  12. handle features from soft separately from user provided features

    Azedine Zoufir committed Jun 30, 2023
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  13. add mix versions for AFFY_JUSTRMA_RAW, AFFY_JUSTRMA_NORM and READ_FRO… 

    …M_SOFT
    Azedine Zoufir committed Jun 30, 2023
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  14. make query GSE about downloading SOFT matrices and not about non-affy

    Azedine Zoufir committed Jun 30, 2023
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  15. change logic to set ch_matrix_for_differential = ch_norm for all non-… 

    …rnaseq
    Azedine Zoufir committed Jun 30, 2023
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  16. simplify processing input to reporting modules

    Azedine Zoufir committed Jun 30, 2023
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  17. fix typo (was combining twice)

    Azedine Zoufir committed Jun 30, 2023
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  18. clean up commented code blocks

    Azedine Zoufir committed Jun 30, 2023
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Commits on Jul 25, 2023

  1. Merge branch 'dev' into soft_matrix_support

    @pinin4fjords
    pinin4fjords committed Jul 25, 2023
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Commits on Jul 26, 2023

  1. swap geoquery from local to nf-core module in main workflow

    Azedine Zoufir committed Jul 26, 2023
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  2. install geoquery/getgeo as nf-core module

    Azedine Zoufir committed Jul 26, 2023
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  3. add geoquery in modules.json

    Azedine Zoufir committed Jul 26, 2023
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Commits on Aug 25, 2023

  1. remove usage of alias for GEOQUERY_GETGEO

    Azedine Zoufir committed Aug 25, 2023
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  2. remove read_from_soft files from local folder

    Azedine Zoufir committed Aug 25, 2023
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  3. fix spacing in conf/modules.config 

    Co-authored-by: Jonathan Manning <jonathan.manning@deeplife.co>
    @azedinez @pinin4fjords
    azedinez and pinin4fjords committed Aug 25, 2023
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  4. remove querygse as external arg in conf/modules.config 

    Co-authored-by: Jonathan Manning <jonathan.manning@deeplife.co>
    @azedinez @pinin4fjords
    azedinez and pinin4fjords committed Aug 25, 2023
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  5. add querygse as input for channel workflows/differentialabundance.nf 

    Co-authored-by: Jonathan Manning <jonathan.manning@deeplife.co>
    @azedinez @pinin4fjords
    azedinez and pinin4fjords committed Aug 25, 2023
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  6. revert to using ch_query_gse as input channel for GEOQUERY_GETGEO pro… 

    …cess
    Azedine Zoufir committed Aug 25, 2023
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  7. delete join on ch_querygse in workflows/differentialabundance.nf 

    Co-authored-by: Jonathan Manning <jonathan.manning@deeplife.co>
    @azedinez @pinin4fjords
    azedinez and pinin4fjords committed Aug 25, 2023
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  8. delete mixing versions for JUSTRMA_NORM 

    Co-authored-by: Jonathan Manning <jonathan.manning@deeplife.co>
    @azedinez @pinin4fjords
    azedinez and pinin4fjords committed Aug 25, 2023
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Commits on Aug 28, 2023

  1. Correctly refer to matrices from getgeo as norm

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  2. Make sure supplying metadata cols is optional

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  3. Sort out config for SOFT

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  4. prettier

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  5. Fix soft config import

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  6. Fix channel name

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  7. Fix config selector

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  8. Fix channel definition

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  9. Fix CHANGELOG

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  10. Final fixes

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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  11. limit resources for testing

    @pinin4fjords
    pinin4fjords committed Aug 28, 2023
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Commits on Sep 11, 2023

  1. add soft config

    Azedine Zoufir committed Sep 11, 2023
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  2. Remove rogue tab

    @pinin4fjords
    pinin4fjords committed Sep 11, 2023
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  3. Merge branch 'soft_matrix_support' of github.com:nf-core/differential… 

    …abundance into soft_matrix_support
    @pinin4fjords
    pinin4fjords committed Sep 11, 2023
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