nf_reporter

Integrate metagenomic reports.

Authors: Colin Davenport, Lisa Hollstein, Janno Peilert

Goal - metagenomic data integration:

• integrate multiple metagenomic reports into one table.
• So species found by raspir should be listed as "raspir_positive" or "raspir_negative" in the haybaler table (in a new column)
• later, species found by krakenuniq and metaphlan should be treated simularly (new column in haybaler)
• provide multiple views of this table for different stakeholders

How does this fit into Wochenende/Haybaler ?

• nf_reporter should be run after Wochenende and Haybaler (i.e. using wochenende_postprocess.sh ) have been completed
• The original Haybaler scripts don't need any more changes
• We just refine the voluminous but unintegrated data output by wochenende_postprocess.sh to help users.

Run

Run nextflow script on a server where R is installed

nextflow run nf_integrate.nf

Install

Setup nextflow as per their website

Perhaps add pandas

conda deactivate
python -m pip --user pandas=1.2.5

Get example files

bash get_example_data.sh

Merging options

ideally after raspir

├── raspir
│   ├── 1_sm_R1.ndp.trm.s.mm.dup.mq30.raspir_final_stats.csv
│   ├── 2_sm_R1.ndp.trm.s.mm.dup.mq30.raspir_final_stats.csv
│   ├── 3_sm_R1.ndp.trm.s.mm.dup.mq30.raspir_final_stats.csv
│   ├── 4_sm_R1.ndp.trm.s.mm.dup.mq30.raspir_final_stats.csv
│   └── 5_sm_R1.ndp.trm.s.mm.dup.mq30.raspir_final_stats.csv
├── README.md
└── reporting
    └── haybaler
        ├── 1_sm_R1.ndp.trm.s.mm.dup.mq30.bam.txt.rep.us.csv
        ├── 2_sm_R1.ndp.trm.s.mm.dup.mq30.bam.txt.rep.us.csv
        ├── 3_sm_R1.ndp.trm.s.mm.dup.mq30.bam.txt.rep.us.csv
        ├── 4_sm_R1.ndp.trm.s.mm.dup.mq30.bam.txt.rep.us.csv
        ├── 5_sm_R1.ndp.trm.s.mm.dup.mq30.bam.txt.rep.us.csv

.
└── fit_results
    └── output
        ├── 1_sm_R1.ndp.trm.s.mm.dup.mq30.calmd_subsamples_results.csv
        ├── 2_sm_R1.ndp.trm.s.mm.dup.mq30.calmd_subsamples_results.csv
        ├── 3_sm_R1.ndp.trm.s.mm.dup.mq30.calmd_subsamples_results.csv
        ├── 4_sm_R1.ndp.trm.s.mm.dup.mq30.calmd_subsamples_results.csv
        └── 5_sm_R1.ndp.trm.s.mm.dup.mq30.calmd_subsamples_results.csv