Code

Sfitz by readgroup and add FastQC#62

Code

Merged

sorelfitzgibbon merged 46 commits intomainuclahs-cds/pipeline-generate-SQC-BAM:mainfrom sfitz-by-readgroupuclahs-cds/pipeline-generate-SQC-BAM:sfitz-by-readgroupCopy head branch name to clipboardJul 19, 2024

+796-97

Commits

Commits on Jun 16, 2024

• process by readgroup in progress

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  d0d3a7b

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• standardize algorithms to algorithm

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  adb0591

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• samtools stats by readgroup

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  ad00e21

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• update changelog

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  046ce02

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• fix mislabel

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  07b5458

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• revert unintentional resource changes

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  eb422cc

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• add fastqc

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  ae43ccd

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• add fastqc module

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  68cf4b4

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• use process_afterscript

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  b738e51

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• update changelog

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  27f1581

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• update nftest for fastqc

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  1c922f9

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• fix nftest path

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  dff3a7a

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• merge with sfitz-by-readgroup complete and tested

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  dbf3a01

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• use fastqc docker with samtools

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  9fd01e9

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• fastqc by readgroup

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  c5407f8

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• nftest paths updated

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  8653bbc

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• refactor channels

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  20085c3

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• add hg003 to NFTest

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  b34451e

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• update samtools

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  d049c14

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• pull main - samtools update

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  53632de

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• use fastqc docker with samtools

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  committed
  19b68a2

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• add fastqc resource allocations

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  0e2c3df

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• add fastqc threading and adjust resources

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  f95d47e

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• add fastqc

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Commits on Jun 17, 2024

• add fastqc to metadata.yaml

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Commits on Jun 20, 2024

• Bump the pipeline-submodules group with 2 updates

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  authored and

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  cc38b86

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• Merge branch 'main' into sfitz-by-readgroup

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  9c9e207

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• add final newline

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  198b40c

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Commits on Jun 24, 2024

• update readme

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  91bf337

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• update nftest.yml

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  4e2b724

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Commits on Jun 25, 2024

• parameterize fastqc and add max gps to stats

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  01b50bf

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• sanitize library ID

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  e61b1ac

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• update test configs

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  e6d0200

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• change process input variable names

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  91f47d3

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• add slurm logs and extra test files to .gitignore

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  a2f0489

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Commits on Jun 26, 2024

• update readme

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  fae512d

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• update comments

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  ecf44dd

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• adjust run level triggers

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  206c7e9

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• adjust log filename

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  8587520

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• update nftests

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  137874f

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• fix test name

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Commits on Jun 27, 2024

• remove out of date comments

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  86cc4b2

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• change process names

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  8fd7119

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• rename bamqc_outformat to bamqc_output_format

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• rename bamqc_outformat to bamqc_output_format

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  2a63bb4

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• remove fastqc as default

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  committed
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