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Adds updated exclusion criterion for transcripts #3

Merged

cgpu merged 63 commits into aws from update-exclusion-criterion

May 8, 2020

cgpu commented Apr 29, 2020 •

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This PR updates the first filtering criterion for keeping or discarding transcripts based on zero values in RSEM abundance estimates, as discussed with @karleg and @pnrobinson.

The suggestion was to take into account the N, number of individuals in the minority class (control or case) and use a percentage of this class (eg. 10%) to set the tolerated fraction of observed zeros across this class's measured subjects.

The code below describes how the exclusion criterion should be implemented and applied:

num.case=length(case)
num.control=length(control)
N_sample=min(num.case,num.control)
countsData=countsData[rowSums(countsData[,3:(2+num.control)]>0)>=N_sample*0.9,]
countsData=countsData[rowSums(countsData[,(2+num.control+1):ncol(countsData)]>0)>=N_sample*0.9,]


          Adds updated exclusion criterion for transcripts

9526a2d

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          Replaces outdated param name to latest (aka "zeroes_threshold")

92c6661

Adresses this: https://github.com/TheJacksonLaboratory/coronavirus-nf/pull/3/files#r417257361

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cgpu added 3 commits

April 29, 2020 13:19


          Corrects zeroes_threshold default, sets it to 0.9

5e9890b

Thanks for catching this @karleg


          Corrects typo essage->messsage

3f4139b


          Changes >= to > strictly greater

69fb678

Author

cgpu commented Apr 29, 2020

Also I would change the condition to strictly greater (> instead of >=) because we want it to take effect only if we have more than 10 samples in each condition

👍 implemented in 69fb678.

cgpu requested a review from karleg

April 29, 2020 15:06

karleg approved these changes

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cgpu added 6 commits

April 29, 2020 16:28


          Changes hbadeals cpus to 32

f913b46


          Refactoring; Simpler paraller with each

557ed5c


          Adds more validation of HBA-DEALS input

010edf3

- Updated docker image sha256:ff3d87fbeb1d5dbabae1d3adcd81cfa284ba291a61ea993491fad6862ec9cb47
- Adresses incidents of SRR samples failing eg. because not paired-end
- Re-ordering for metadata after filtering out SRR that failed in previous steps


          Adds ignore; Addresses single end SRR - 255 exit in trimgalore

b9da262


          Corrects tar -c -> -x for decompression

27b1c5b


          Refactoring; tar czvf moves where .collect() is (.iso.res)

ef68e77

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cgpu added 3 commits

April 30, 2020 07:25


          Removes redundant files from output

eeb0485


          Increases retry count

a2a3fe2


          Fixes tiny typo

432edc4


          Adds @commit hash for HBA-DEALS repo for reproducibility

f3d738e

karleg reviewed

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          Reduces vCPU 32->30 (leave some for house keeping tasks)

1750d2c

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cgpu and others added 24 commits

May 7, 2020 02:32


          Updates HBA-DEALS param names (change introduced with 03497b6 )

a038fdb


          Pseudo PR to view changes in resource allocation (#8)

2f7c118

* Allocates 10 of 32 cpus for hbadeals() (with 4 of 32 cpus it worked)

CloudOS link with successful job with 4 vCPUS:
https://cloudos.lifebit.ai/public/jobs/5eb3bc3d1795470103deadba

* Triggers first tests for fork; Adds https:// (secure)


          Cleaning branch; Deletes test data

6c1311f


          Absorbs resource alloc changes from branch test-less-resources

6bf11e6


          Fix nf-core lint errors (#9)

a5493cb

* Applies linting suggestions from failed linting tests

* Adds asset to remove inline <img> html

* Adds dev container (nf-core) style (to keep nf-core tests happy)

* Sets reads to default:false

* Adds sarek logic; include hbadeals in tools

* Migrates processes of label:hbadeals inside rsem if clause

* Refactoring hbadeals processes and channels positions


          Removes depricated param skip_hbadeals

4fdf6e5


          Absorbs changes from fix-nf-lint branch into update-exclusion-criterion

defd15b


          Removes outdated param.skip_hbadeals from ci.yml

2482ef6


          Removes outdated param.skip_hbadeals from ci.yml

a3b1767


          Sets resources for HBA-DEALS to 18 of 32

d6f568e


          Adds tools in help message

845b273


          Adds user message that HBA-DEALS only runs when:RSEM

244dd4e


          Removes deprecated param from help

7d3ca6b


          Changes to snake_case: accessionList -> accession_list

142804e


          Replaces accessionList to acccession_list in ipynb

b562031


          Eliminates camelCase residues from channel names

99627f9


          Remove extra line

7ca5a6c


          Minor trims, whitespace, new lines

509b870


          Cleans parameters for hbadeals


          Corrects phrasing of message

5dcf621


          Adds def checkParameterExistence(it, list)

95d4238


          Restores container to updated

d05d930


          Removes nf-core linting

17ac537


          Pins pipeline container to lifebitai/nf-core-rnaseq:1.4.3.rsem

7be0d26

Author

cgpu commented May 8, 2020

@karleg @adeslatt @pnrobinson Tests passing, going forth with merge!

cgpu merged commit 4b7414c into aws

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