Hs metrics #313
Hs metrics #313
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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.
This PR is against the
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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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@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:
you can reach out on nf-core slack |
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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.
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
The module: collecthsmetrics is now available from modules/nf-core