Soft matrix support #136

azedinez · 2023-06-15T16:29:49Z

Added support for non Affymetrix platforms via download of SOFT matrices directly from GEO. These matrices are already quantile normalised, but to be comparable to the output of JUSTRMA, a log2 transformation is applied (if applicable).

Tested with added profile test_soft. Also tested on a couple of beadchip mouse datasets.

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!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

…y] track

… array platform)

github-actions · 2023-06-15T16:31:29Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit 45dd543

+| ✅ 158 tests passed       |+

✅ Tests passed:

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Run details

nf-core/tools version 2.9
Run at 2023-09-11 15:49:36

Co-authored-by: Jonathan Manning <[email protected]>

…cess

Co-authored-by: Jonathan Manning <[email protected]>

azedinez · 2023-08-25T15:18:51Z

Apologies for delay in addressing this. I believe I've addressed all your comments but let me know if I need to address more stuff. Otherwise feel free to merge.

pinin4fjords · 2023-08-28T10:41:49Z

@azedinez I had to make a number of fixes and tweaks to make this actually work (and the tests are now running in CI). Could you please test locally to make sure outputs are as you would like?

azedinez · 2023-09-11T15:41:33Z

@pinin4fjords Tested locally and runs. All output looks as expected. I have just added the soft config to the pipeline for convenience.

…abundance into soft_matrix_support

pinin4fjords

Great- we've got there. Thanks for the work @azedinez !

Azedine Zoufir added 28 commits June 13, 2023 10:46

R script read from soft matrix

618a90d

add read_from_soft process to pipeline

5555340

add configuration for read_from_soft process

1d2f9ec

incorporate read from soft process into workflow

0b48cef

add querygse as an input parameter to workflow

4b4aad6

add querygse to schema

27ec512

add 'non_affy_array' as possible value for study type param

cfa223c

fixing configs for read_from_soft process

8e32b08

fix geoquery container url in read_from_soft.nf

3af5ed3

remove raw matrix processing for [non_affy_array] track

1227674

remove raw matrix processing for [non_affy_array] track

baaf791

attempt to fix premature completion of pipeline

e1ff15c

attempt to fix premature completion of pipeline

3b773a8

debug around contrasts & matrix filter

5068295

debug around contrasts & matrix filter

03e30fd

debug matrix input processing for exploratory plots in [non_affy_arra…

054275a

…y] track

do not filter matrix in [non_affy_array] track

4092a93

revert debug and apply log2 transformation to READ_FROM_SOFT output

7cc0a17

add test SOFT matrix track config

8df1f28

add test SOFT matrix track config

b4b8f8b

fix typo in config file

735999a

add extra input to READ_SOFT_MATRIX to process metacolumns (differ by…

ab1cb71

… array platform)

fix typo in config

af0518e

fix typo in config

872023d

fix parameter name in read_soft_matrix

e7bfdc6

fix parameter name in read_soft_matrix

52929b3

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

94b9b26

update docs

ed95ab4

azedinez requested a review from pinin4fjords June 15, 2023 16:29

Azedine Zoufir and others added 8 commits August 25, 2023 15:51

remove usage of alias for GEOQUERY_GETGEO

3fa023e

remove read_from_soft files from local folder

6da3cac

fix spacing in conf/modules.config

db1ada5

Co-authored-by: Jonathan Manning <[email protected]>

remove querygse as external arg in conf/modules.config

eaf597f

Co-authored-by: Jonathan Manning <[email protected]>

add querygse as input for channel workflows/differentialabundance.nf

4a419e4

Co-authored-by: Jonathan Manning <[email protected]>

revert to using ch_query_gse as input channel for GEOQUERY_GETGEO pro…

2f4f6fc

…cess

delete join on ch_querygse in workflows/differentialabundance.nf

843c653

Co-authored-by: Jonathan Manning <[email protected]>

delete mixing versions for JUSTRMA_NORM

b782445

Co-authored-by: Jonathan Manning <[email protected]>

pinin4fjords added 11 commits August 28, 2023 09:36

Correctly refer to matrices from getgeo as norm

dc1c337

Make sure supplying metadata cols is optional

fed96cc

Sort out config for SOFT

62feb14

prettier

248756c

Fix soft config import

281a18e

Fix channel name

430f530

Fix config selector

33389fc

Fix channel definition

cfaf8eb

Fix CHANGELOG

1c842bb

Final fixes

9790859

limit resources for testing

abed797

add soft config

823b4cd

pinin4fjords added 2 commits September 11, 2023 16:47

Remove rogue tab

6e2480c

Merge branch 'soft_matrix_support' of github.com:nf-core/differential…

45dd543

…abundance into soft_matrix_support

pinin4fjords approved these changes Sep 11, 2023

View reviewed changes

azedinez merged commit 8d61010 into dev Sep 12, 2023

azedinez deleted the soft_matrix_support branch September 12, 2023 08:12

pinin4fjords mentioned this pull request Oct 6, 2023

Rlog + other small fixes #164

Merged

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pinin4fjords added this to the 1.3.0 milestone Oct 10, 2023

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Soft matrix support #136

Soft matrix support #136

azedinez commented Jun 15, 2023 •

edited

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github-actions bot commented Jun 15, 2023 •

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✅ Tests passed:

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azedinez commented Aug 25, 2023

pinin4fjords commented Aug 28, 2023

azedinez commented Sep 11, 2023

pinin4fjords left a comment

Soft matrix support #136

Soft matrix support #136

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azedinez commented Jun 15, 2023 • edited Loading

PR checklist

github-actions bot commented Jun 15, 2023 • edited Loading

nf-core lint overall result: Passed ✅

✅ Tests passed:

Run details

azedinez commented Aug 25, 2023

pinin4fjords commented Aug 28, 2023

azedinez commented Sep 11, 2023

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azedinez commented Jun 15, 2023 •

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`nf-core lint` overall result: Passed ✅