Code

Soft matrix support#136

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azedinez merged 77 commits intodevnf-core/differentialabundance:devfrom soft_matrix_supportnf-core/differentialabundance:soft_matrix_supportCopy head branch name to clipboardSep 12, 2023

+445-32

Commits

Commits on Jun 13, 2023

• R script read from soft matrix

  

  Azedine Zoufir

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  618a90d

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• add read_from_soft process to pipeline

  

  Azedine Zoufir

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• add configuration for read_from_soft process

  

  Azedine Zoufir

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  1d2f9ec

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• incorporate read from soft process into workflow

  

  Azedine Zoufir

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  0b48cef

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• add querygse as an input parameter to workflow

  

  Azedine Zoufir

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  4b4aad6

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• add querygse to schema

  

  Azedine Zoufir

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• add 'non_affy_array' as possible value for study type param

  

  Azedine Zoufir

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  cfa223c

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Commits on Jun 14, 2023

• fixing configs for read_from_soft process

  

  Azedine Zoufir

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  8e32b08

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• fix geoquery container url in read_from_soft.nf

  

  Azedine Zoufir

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  3af5ed3

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• remove raw matrix processing for [non_affy_array] track

  

  Azedine Zoufir

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  1227674

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• remove raw matrix processing for [non_affy_array] track

  

  Azedine Zoufir

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  baaf791

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• attempt to fix premature completion of pipeline

  

  Azedine Zoufir

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  e1ff15c

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• attempt to fix premature completion of pipeline

  

  Azedine Zoufir

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  3b773a8

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• debug around contrasts & matrix filter

  

  Azedine Zoufir

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  5068295

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• debug around contrasts & matrix filter

  

  Azedine Zoufir

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  03e30fd

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• debug matrix input processing for exploratory plots in [non_affy_array] track

  

  Azedine Zoufir

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• do not filter matrix in [non_affy_array] track

  

  Azedine Zoufir

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Commits on Jun 15, 2023

• revert debug and apply log2 transformation to READ_FROM_SOFT output

  

  Azedine Zoufir

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  7cc0a17

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• add test SOFT matrix track config

  

  Azedine Zoufir

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• add test SOFT matrix track config

  

  Azedine Zoufir

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  b4b8f8b

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• fix typo in config file

  

  Azedine Zoufir

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  735999a

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• add extra input to READ_SOFT_MATRIX to process metacolumns (differ by array platform)

  

  Azedine Zoufir

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  ab1cb71

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• fix typo in config

  

  Azedine Zoufir

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  af0518e

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• fix typo in config

  

  Azedine Zoufir

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  872023d

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• fix parameter name in read_soft_matrix

  

  Azedine Zoufir

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  e7bfdc6

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• fix parameter name in read_soft_matrix

  

  Azedine Zoufir

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  52929b3

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• change column names to GSM ids in configuration, to match SOFT format

  

  Azedine Zoufir

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  94b9b26

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• update docs

  

  Azedine Zoufir

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Commits on Jun 16, 2023

• update docs

  

  Azedine Zoufir

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• NA treatment when determining if log transformation needs to be applied

  

  Azedine Zoufir

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• NA treatment when determining if log transformation needs to be applied

  

  Azedine Zoufir

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  5308d7c

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Commits on Jun 28, 2023

• fix typo in test prior to differential process

  

  Azedine Zoufir

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  2dc1a41

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• [automated] Fix linting with Prettier

  nf-core-bot

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Commits on Jun 30, 2023

• put changes back into v1.3.0

  

  Azedine Zoufir

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  738d5bb

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• Merge branch 'soft_matrix_support' of https://github.com/nf-core/differentialabundance into soft_matrix_support

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  Azedine Zoufir

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  6aec513

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• replace new study type [non_affy_array] by [geo_soft_file]

  

  Azedine Zoufir

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  5445817

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• remove [querygse] and [features_metadata_cols] as input to read_soft modules and use as params instead

  

  Azedine Zoufir

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  434c810

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• Merge branch 'dev' into soft_matrix_support

  azedinez

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  572e46c

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• fix linting/indents in read_soft_matrix.R

  

  Azedine Zoufir

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  718c0b3

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• Merge branch 'soft_matrix_support' of https://github.com/nf-core/differentialabundance into soft_matrix_support

  

  Azedine Zoufir

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  70781d5

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• remove usage of 'non affymetrix' in docs and stress that's is a different use case

  

  Azedine Zoufir

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• name input channel for soft rather than generic

  

  Azedine Zoufir

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  bf54aa8

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• handle features from soft separately from user provided features

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  azedinez

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  pinin4fjords

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  38e7020

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• handle features from soft separately from user provided features

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  azedinez

  and

  pinin4fjords

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  0f41d6f

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• handle features from soft separately from user provided features

  

  Azedine Zoufir

  committed
  0916ee1

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• add mix versions for AFFY_JUSTRMA_RAW, AFFY_JUSTRMA_NORM and READ_FROM_SOFT

  

  Azedine Zoufir

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  b0c46ab

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• make query GSE about downloading SOFT matrices and not about non-affy

  

  Azedine Zoufir

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  2c0158c

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• change logic to set ch_matrix_for_differential = ch_norm for all non-rnaseq

  

  Azedine Zoufir

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  0aee2fa

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• simplify processing input to reporting modules

  

  Azedine Zoufir

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  45ec150

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• fix typo (was combining twice)

  

  Azedine Zoufir

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  7983d4e

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• clean up commented code blocks

  

  Azedine Zoufir

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Commits on Jul 25, 2023

• Merge branch 'dev' into soft_matrix_support

  pinin4fjords

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Commits on Jul 26, 2023

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

  

  Azedine Zoufir

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  d16b9b7

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• install geoquery/getgeo as nf-core module

  

  Azedine Zoufir

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  6b5a9e7

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• add geoquery in modules.json

  

  Azedine Zoufir

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  3e579e3

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Commits on Aug 25, 2023

• remove usage of alias for GEOQUERY_GETGEO

  

  Azedine Zoufir

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  3fa023e

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• remove read_from_soft files from local folder

  

  Azedine Zoufir

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  6da3cac

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• fix spacing in conf/modules.config

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  azedinez

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  pinin4fjords

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  db1ada5

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• remove querygse as external arg in conf/modules.config

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  azedinez

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  pinin4fjords

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  eaf597f

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• add querygse as input for channel workflows/differentialabundance.nf

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  azedinez

  and

  pinin4fjords

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  4a419e4

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• revert to using ch_query_gse as input channel for GEOQUERY_GETGEO process

  

  Azedine Zoufir

  committed
  2f4f6fc

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• delete join on ch_querygse in workflows/differentialabundance.nf

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  azedinez

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  pinin4fjords

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  843c653

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• delete mixing versions for JUSTRMA_NORM

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  azedinez

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  pinin4fjords

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Commits on Aug 28, 2023

• Correctly refer to matrices from getgeo as norm

  pinin4fjords

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  dc1c337

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• Make sure supplying metadata cols is optional

  pinin4fjords

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• Sort out config for SOFT

  pinin4fjords

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  62feb14

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• prettier

  pinin4fjords

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  248756c

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• Fix soft config import

  pinin4fjords

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  281a18e

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• Fix channel name

  pinin4fjords

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  430f530

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• Fix config selector

  pinin4fjords

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• Fix channel definition

  pinin4fjords

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  cfaf8eb

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• Fix CHANGELOG

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• Final fixes

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• limit resources for testing

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Commits on Sep 11, 2023

• add soft config

  

  Azedine Zoufir

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  823b4cd

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• Remove rogue tab

  pinin4fjords

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  6e2480c

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• Merge branch 'soft_matrix_support' of github.com:nf-core/differentialabundance into soft_matrix_support

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