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Hs metrics #313

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Hs metrics #313

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RogerHw
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@RogerHw RogerHw commented May 26, 2023

The module: collecthsmetrics is now available from modules/nf-core

Addition of Markduplicates module for each aligner
Modification: HS metrics
collecthsmetrics module content
Include module twice: Qualimap (Before and After Markduplicates in the BAM file) Add module Qualimap into the workflow twice (QUALIMAP and QUALIMAP2 

The syntax of markduplicates module was corrected. 

HS metrics was also corrected with an else statment to avoid the use of the module in case that BED file is not included as an input.
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @RogerHw,

It looks like this pull-request is has been made against the RogerHw/Trainee master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the RogerHw/Trainee dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@RogerHw RogerHw changed the base branch from master to dev May 26, 2023 17:50
The new modules were included. ' collecthsmetrics', and 'createsequenceddictionary'
Parameter to execute the module hsmetrics in case that bed file is provided
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@sateeshperi
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@RogerHw quick question, have you used nf-core tools to install the new module? as i am not seeing those files other than addition to modules.json

@RogerHw
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RogerHw commented May 30, 2023

@RogerHw quick question, have you used nf-core tools to install the new module? as i am not seeing those files other than addition to modules.json

Hi! I'm sorry, I´m new at Git / Nextflow, I did the pull request in the main but I actually wanted to do it in the dev branch. Yes I installed th HS metrics module with nf-core tools, is just that I didn't upload the files.

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cool...let me help you....now your PR is against dev so that's good. some of the next steps are:

  1. git pull current dev and make sure it is up to date
  2. finish making your changes then run prettier --check . and nf-core lint
  3. make sure all lint tests pass and commit your changes and push

you can reach out on nf-core slack #methylseq channel if you need more help

@RogerHw
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RogerHw commented May 30, 2023

cool...let me help you....now your PR is against dev so that's good. some of the next steps are:

  1. git pull current dev and make sure it is up to date
  2. finish making your changes then run prettier --check . and nf-core lint
  3. make sure all lint tests pass and commit your changes and push

you can reach out on nf-core slack #methylseq channel if you need more help
Sure! thank you so much :)

RogerHw added 12 commits June 1, 2023 13:30
Change HS metrics module, adition of the new parameters (Dictionary and the bai input)
Include the modules
Main process of module
module hs metrics
meta file
collecths metrics module
Corrections in the code to include the HS metrics into the multiqc module.
@sateeshperi sateeshperi added the WIP Work in progress label Jun 1, 2023
RogerHw added 13 commits June 5, 2023 14:07
Input of create sequence dictionary module is now corrected
Addition of bait and target intervals configuration
bait and target intervals are now set to false
Previously, the parameters were added manually, now the file is updated using nf-core schema build tool.
corect a miss matched bracket.  ' Qualimap as Qualimap2' was deleated and the multiqc channel from this module was also deleated.
Dictionary now is created directly as a value channel
of method instead of value were used to decleared the channels
Modification in the dictionary channel, instead of decleared with channel.of method is  now collected.
New channels were created to map the correct elements for the HS metrics module.
Delete redundant code. map function wasn't really usefull
Ch_fasta and ch_fai are now value channels and are mapped by map function. Also, combine function was used to  merge the four channels in one
@RogerHw RogerHw requested a review from a team as a code owner January 5, 2024 20:41
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