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Nucleovar Pre-Release Notes #14

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Nucleovar Pre-Release Notes #14

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@rnaidu rnaidu commented Oct 1, 2024 •
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rnaidu and others added 30 commits December 20, 2023 14:28
@rnaidu
Redownloaded nf-core vardictjava and wrote code to match inputs witho…
09676dc 
…ut changing original module.
@rnaidu
Pushing progress on vardictjava.nf
820c639
@rnaidu
Cleaned up unused code chunks, add fasta, bed, and fai CLI args, and …
530e62a 
…added parameter validation/checking statements in WorkflowNucleovar.groovy
@rnaidu
added CLI arguments to nextflow_schema.json to pass linting checks.
68f343c
@rnaidu
adding linting.yml file (unchanged) to pass linting checks.
89251a1
@rnaidu
adding updated nf-core modules to pass linting checks.
b7f3118
@rnaidu
keeping workingd directory up to date to pass lint checks.
67dc6e6
@rnaidu
modified inputs to match input cardinality for vardictjava
712ba3d
@rnaidu
Merge branch 'feature/call_variants' of https://github.com/mskcc-omic…
0e734f5 
…s-workflows/nucleovar into feature/call_variants

keeping branches up to date between cluster and local
@rnaidu
keeping working branch up to date
03b570d
@rnaidu
added CLI options for vardictjava, module is successfully working in …
060f8fb 
…single sample mode.
@rnaidu
Added mutect1 task.ext args in modules.config
2e5185a
@rnaidu
added code to prepare inputs for mutect1 module and added call to mut…
fa0452b 
…ect1 module (commented out until mutect1 PR has been reviewed)
@rnaidu
created local module for vardict_filtering (utilizing post-processing…
e9def4e 
… variant calling docker image) and added to call_variants.nf subworkflows with necessary args
@rnaidu
added vardict_filter module and changed acceptance criteria of input …
0788d06 
…BAM files from ArrayList to List type in vardictjava module
@rnaidu
updated vardict_filter.nf (successfully tested locally on single samp…
000cc68 
…le mode)
@rnaidu
pushing code changes to vardict_filter.nf-- updated module and now su…
3d53ba5 
…ccessfully working in single and paired sample mode
@rnaidu
pushing current work
8d6ea31
@rnaidu
creating two separate subworkflows for single sample and case control…
a386830 
… calling and added conditional statement in nucleovar.nf to trigger pipeline depending on number of samples as input. Also cleanup of random test data and directories
@rnaidu
pushing work I have so far
1bbd048
@rnaidu
pushing vardictjava
fe26fbe
@rnaidu
cleaning up null directory
d8b7576
@rnaidu
pushing latest commits
967eae9
@rnaidu
removing subworkflows not being used in nucleovar
a569901
@rnaidu
pushing updated work to begin testing on terra
5e60d0e
@rnaidu
pushing updated work for cluster testing
2de2d3d
Template update for nf-core/tools version 2.13.1
2f87623
Merge branch 'TEMPLATE' into feature/call_variants_lsf
677b945
running on cluster
c9eb622
@rnaidu
pushing work so far with using the updated samplesheet
5b3ab08
@rnaidu
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rnaidu commented Oct 10, 2024

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