[Do not merge!] Pseudo PR for first release #28

mashehu · 2024-08-02T09:03:24Z

Do not merge! This is a PR of dev compared to first release for whole-pipeline reviewing purposes. Changes should be made to dev and this PR should not be merged into first-commit-for-pseudo-pr!

…o isoquant_dev

…r to resolve linting issues

…regardless of if the user chooses to trim files or not

…rrors

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

mashehu

just some smaller things, will approve the other PR.

mashehu · 2024-09-27T06:35:12Z

.gitignore

@@ -6,3 +6,8 @@ results/
 testing/
 testing*
 *.pyc
+test.sh
+params.yml


Why do you explicitly ignore params and the samplesheet file?

During development, we often worked out of the github directory and would place the samplesheet and parameter files in there, so to remove the chance of an accidental commit of either one we went ahead and added them here.

mashehu · 2024-10-02T08:57:12Z

assets/scnanoseq_diagram.png

very nice tube map. small nit-picky thins you can ignore:

can you please name it something like scnanoseq_tube_map, so we can pick automatically pick it up for some future nf-core things.

can you also provide an svg version, which makes it easier for collaborators to edit and extend the map

can you trie to center the "Alignment" and the "Barcode correction" nodes in the middle of their respective curves

In the legend, I would flip the symbol for File Output 180 degrees (so it ends in the horizontal bar, following the reading direction)

might be an optical illusion, but are the Count QC nodes correctly horizontally centered between the curves before and after them?

I went ahead and tried to address all these with commit 86284fa. Let me know if you see any missing/ anything else

docs/output.md

mashehu · 2024-10-02T09:04:32Z

docs/usage.md

 ```

-### Full samplesheet
+`cell_count` refers to the expected number of cells for each sample, which can vary from sample to sample.


is that value relevant for a specific processing step?

It is -- cell count is utilized by the BLAZE barcode caller as a guide to determine the 'correct' number of barcodes that need to be called

i would clarify that here (or point to the relevant section in the docs)

I combined this fix with the point below. We have a table describing the columns so I added the expanded description in there (commit 891b67d)

docs/usage.md

mashehu · 2024-10-02T09:13:58Z

workflows/scnanoseq.nf

+    blaze_whitelist = file("$baseDir/assets/whitelist/3M-february-2018.zip")
+}
+else{
+    blaze_whitelist = file("$baseDir/assets/whitelist/737K-august-2016.txt.zip")


shouldn't then be 10X_5v2 the default value for barcode_format?

Yeah it does read like that, I think it may make more sense to turn the second else into an else if (params.barcode_format.equals("10X_5v2") for readability, since this param can only be one of those two values anyway so it makes it more clear

Tried to address this with commit c082e20

workflows/scnanoseq.nf

…t as a parameter overrides the default whitelist used by the pipeline

atrull314 · 2024-10-03T13:30:04Z

Hi @mashehu,

I believe I managed to address all points, let me know if there's anything missing or if there's any other issues!

Thanks,
Austyn

mashehu · 2024-10-03T13:40:08Z

All good now from my side! 👍🏻

atrull314 · 2024-10-03T13:46:25Z

Awesome, thank you so much!

So as far as activating zenodo. Is that just a post in the pipeline-maintainers channel once we merge into the master branch or can that be done before the merge?

mashehu · 2024-10-03T14:11:57Z

zenodo is already activated. so as soon as you make a release, you will get your DOI

atrull314 and others added 30 commits September 5, 2023 11:29

Merge branch 'isoquant_dev' of https://github.com/U-BDS/scnanoseq int…

adb0208

…o isoquant_dev

Removing debug print

e63c1df

Fixing syntax in modules.conf for base modules

643a372

Adding the ability to merge replicates

f15260e

Reducing requirements for minimap2_index

fd95b1c

Updating nf-core template

e48b020

Merge pull request #5 from U-BDS/isoquant_dev

316136c

Removing enable_conda from local modules and updating modules in orde…

e62bc27

…r to resolve linting issues

Tweaking version to see if that resolves linting error

02eed9d

Changing outdirs for minimap bams

e58f12a

Fixing issues with multiqc introduced by template updates

ee196a7

Updating BLAZE scripts

25e3301

Removing hardcoded cpus in BLAZE config

71cb5a0

Changing preextract fastq to take in zip files

1d7464d

tool versioning updates

9b2f33a

removing depracated module and minor clean-ups

4b8ae45

added minimal test config

4643910

close issue #4

a33a43b

fixing issue with channels for preextract zip file

fb36eb8

Rewriting modules config

75197d1

Correcting issues in workflow so that it passes zipped fastqs around …

70eaa51

…regardless of if the user chooses to trim files or not

Correcting processes that show up as 'no matching config selector'

1071e0a

Removing unused module imports

c336588

Further cleanup of modules config

f527735

Fixing PREPARE_GTF missing selector warning

9fb8c38

Fixing formatting that was causing issues with linting

c911f71

Reformatting the multiqc reports

3e4a923

Fixing EditorConfig linting failures

caea67c

Committing reformatting performed by prettier

4d7c502

Committing first pass at attempting to resolve black python linting e…

3b016ee

…rrors

atrull314 and others added 16 commits September 11, 2024 15:32

Updating based on PR suggestions from LilyAnderssonLee

e373c33

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Updating based on PR suggestions from LilyAnderssonLee

28bd9ec

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Updating based on PR suggestions from LilyAnderssonLee

4333dca

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Updating based on PR suggestions from LilyAnderssonLee

17c5dcd

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Update README.mdUpdating based on PR suggestions from LilyAnderssonLee

9136b5c

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Updating based on PR suggestions from LilyAnderssonLee

a516717

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Fixing linting in README

0b8232f

Adding light logo to linting ignore

b6c3866

Removing need for dummy file to samtools_view

ae824cd

Fixing changelog; Adding TBD for date

0033a1c

Ensuring that fastq parameters are unique

c22d355

Fixing linting

2f5e71b

Upgrading MultiQC so Nanocomp is included in the report

bed7b6e

Update docs/usage.md

1e7e5b1

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Adding small files to tower.yml

7cf2a3e

Fixing tower.yml

9f1ee5e

mashehu commented Oct 2, 2024

View reviewed changes

lianov and others added 6 commits October 2, 2024 12:10

moved nanostat reporting in multiqc

28ecd46

Updating pipeline metro diagram

86284fa

Fixing formatting in output file

9689fdd

Rearranging usage to help with flow

891b67d

Making help message and code more explicit that passing in a whitelis…

c082e20

…t as a parameter overrides the default whitelist used by the pipeline

removed process_long from correct_barcodes

dcd435c

lianov and others added 2 commits October 3, 2024 13:08

added additional custom.config tip

1ef28d1

Fixing linting

596bf4f

atrull314 closed this Oct 7, 2024

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[Do not merge!] Pseudo PR for first release #28

[Do not merge!] Pseudo PR for first release #28

mashehu commented Aug 2, 2024

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mashehu Sep 27, 2024

atrull314 Oct 2, 2024

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mashehu Oct 2, 2024

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mashehu commented Oct 3, 2024

[Do not merge!] Pseudo PR for first release #28

[Do not merge!] Pseudo PR for first release #28

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