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CHANGELOG.md

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CCBR GATK4 WES Pipeline

Stuctural Changes

moved pipeline/config to / moved pipeline/workflow to / moved pipeline/resources to / moved pipeline/scripts to /workflow/scripts

NOTE: delete pipeline/run.sh and remove pipeline/ directory after creating wrapper script

Before:

CCBR_GATK4_Exome_Seq_Pipeline/
├── pipeline
│   ├── config
│   │   ├── cluster.json
│   │   ├── config.json
│   │   └── pairs.mixed.tsv
│   ├── resources
│   │   └── fastq_screen.conf
│   ├── run.sh
│   ├── scripts
│   │   ├── freec
│   │   │   ├── make_freec_config.py
│   │   │   └── py_config
│   │   │       └── config.txt
│   │   ├── get_flowcell_lanes.py
│   │   ├── parse_tn_mode.py
│   │   ├── reformat_bed.py
│   │   └── RScripts
│   │       ├── combineAllSampleCompareResults.R
│   │       ├── combineVerifyBAMIDResults.R
│   │       ├── predictGender.R
│   │       └── sampleCompareAncestoryPlots.R
│   └── workflow
│       ├── rules
│       │   ├── cnv.smk
│       │   ├── ffpe.smk
│       │   ├── germline.smk
│       │   ├── qc.smk
│       │   ├── somatic_snps.common.smk
│       │   ├── somatic_snps.paired.smk
│       │   ├── somatic_snps.tumor_only.smk
│       │   └── trim_map_preprocess.smk
│       └── Snakefile
└── README.md

9 directories, 24 files

After:

CCBR_GATK4_Exome_Seq_Pipeline/
├── config
│   ├── cluster.json
│   ├── config.json
│   └── pairs.mixed.tsv
├── pipeline
│   └── run.sh
├── README.md
├── resources
│   └── fastq_screen.conf
└── workflow
    ├── rules
    │   ├── cnv.smk
    │   ├── ffpe.smk
    │   ├── germline.smk
    │   ├── qc.smk
    │   ├── somatic_snps.common.smk
    │   ├── somatic_snps.paired.smk
    │   ├── somatic_snps.tumor_only.smk
    │   └── trim_map_preprocess.smk
    ├── scripts
    │   ├── freec
    │   │   ├── make_freec_config.py
    │   │   └── py_config
    │   │       └── config.txt
    │   ├── get_flowcell_lanes.py
    │   ├── parse_tn_mode.py
    │   ├── reformat_bed.py
    │   └── RScripts
    │       ├── combineAllSampleCompareResults.R
    │       ├── combineVerifyBAMIDResults.R
    │       ├── predictGender.R
    │       └── sampleCompareAncestoryPlots.R
    └── Snakefile

9 directories, 24 files

TLDR: basically moved things out of pipeline directory.