├── ._wb ├── launcher │ └── docker │ │ ├── config.json │ │ └── run.sh └── tool │ └── phip-flow │ ├── config.json │ └── run.sh ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── bin ├── fit-predict-zscore.py ├── generate-fasta.py ├── merge-counts-stats.py ├── replicate-counts.py ├── run_BEER.Rscript ├── run_edgeR.Rscript ├── validate-peptide-table.py └── validate-sample-table.py ├── data ├── misc │ ├── dag.png │ └── simulated-example │ │ ├── NGS │ │ └── expa │ │ │ ├── sample_0.fastq │ │ │ ├── sample_1.fastq │ │ │ ├── sample_10.fastq │ │ │ ├── sample_11.fastq │ │ │ ├── sample_2.fastq │ │ │ ├── sample_3.fastq │ │ │ ├── sample_4.fastq │ │ │ ├── sample_5.fastq │ │ │ ├── sample_6.fastq │ │ │ ├── sample_7.fastq │ │ │ ├── sample_8.fastq │ │ │ └── sample_9.fastq │ │ ├── nextflow.config │ │ ├── peptide_table.csv │ │ ├── peptide_table_replicates.csv │ │ ├── run_phip_flow.sh │ │ └── sample_table.csv └── pan-cov-example │ ├── NGS │ ├── 4A-rep1-27-library_S27_L001_R1_001.fastq.gz.test.gz │ ├── 4A-rep2-22_S49_L001_R1_001.fastq.gz.test.gz │ ├── 4B-rep1-22_S22_L001_R1_001.fastq.gz.test.gz │ ├── 4B-rep1-27-library_S26_L001_R1_001.fastq.gz.test.gz │ ├── ex11a-beads-35_S87_L001_R1_001.fastq.gz.test.gz │ ├── ex8-rep2-42_S87_L001_R1_001.fastq.gz.test.gz │ ├── expt10B-MEGSUB-4_S4_L001_R1_001.fastq.gz.test.gz │ └── rep1-42_S42_L001_R1_001.fastq.gz.test.gz │ ├── peptide_table.csv │ ├── sample_table_with_beads_and_lib.csv │ ├── sample_table_with_beads_no_lib.csv │ └── sample_table_with_beads_one_emp.csv ├── main.nf ├── nextflow.config ├── templates ├── aggregate_organisms.py ├── generate_index.sh ├── join_organisms.py ├── public_epitope_template.csv ├── sam_to_counts.sh ├── sam_to_stats.sh ├── short_read_alignment.sh └── split_samples.py └── workflows ├── aggregate.nf ├── alignment.nf ├── edgeR_BEER.nf ├── output.nf └── statistics.nf /._wb/launcher/docker/config.json: -------------------------------------------------------------------------------- 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