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Output

Output

All intermediate outputs produced from each module of this pipeline are provided as flat files that can be viewed in a text editor. These files are copied from the root work/ directory created by Nextflow, so if disk space is a concern, this directory should be deleted as it can get quite large.

Directory Structure

The output directories created by the pipeline are named after the module that produced them. Each file output is prefixed with the sample name and suffixed with a short product description.

Files without sample prefixes are a result of aggregation. For example, the files host.removal.stats and trimmomatic.stats provide count matrices for the number of reads discarded as a result of host-dna removal and number of trimmed reads for each sample.

Below is an example of all of the results created with a test run of AMR++.

test_results
├── Alignment
│   ├── BWA_Index
│   │   ├── chr21.fasta.gz.amb
│   │   ├── chr21.fasta.gz.ann
│   │   ├── chr21.fasta.gz.bwt
│   │   ├── chr21.fasta.gz.pac
│   │   ├── chr21.fasta.gz.sa
│   │   ├── megares_database_v3.00.fasta.amb
│   │   ├── megares_database_v3.00.fasta.ann
│   │   ├── megares_database_v3.00.fasta.bwt
│   │   ├── megares_database_v3.00.fasta.pac
│   │   └── megares_database_v3.00.fasta.sa
│   └── SAM_files
│       ├── Deduped
│       │   ├── S1_test.alignment.dedup.sam
│       │   ├── S2_test.alignment.dedup.sam
│       │   └── S3_test.alignment.dedup.sam
│       └── Standard
│           ├── S1_test.alignment.sam
│           ├── S2_test.alignment.sam
│           └── S3_test.alignment.sam
├── HostRemoval
│   └── NonHostFastq
│       ├── S1_test.non.host.R1.fastq.gz
│       ├── S1_test.non.host.R2.fastq.gz
│       ├── S2_test.non.host.R1.fastq.gz
│       ├── S2_test.non.host.R2.fastq.gz
│       ├── S3_test.non.host.R1.fastq.gz
│       └── S3_test.non.host.R2.fastq.gz
├── QC_analysis
│   ├── FastQC
│   │   ├── S1_test_fastqc_logs
│   │   │   ├── S1_test_R1_fastqc.html
│   │   │   ├── S1_test_R1_fastqc.zip
│   │   │   ├── S1_test_R2_fastqc.html
│   │   │   └── S1_test_R2_fastqc.zip
│   │   ├── S2_test_fastqc_logs
│   │   │   ├── S2_test_R1_fastqc.html
│   │   │   ├── S2_test_R1_fastqc.zip
│   │   │   ├── S2_test_R2_fastqc.html
│   │   │   └── S2_test_R2_fastqc.zip
│   │   └── S3_test_fastqc_logs
│   │       ├── S3_test_R1_fastqc.html
│   │       ├── S3_test_R1_fastqc.zip
│   │       ├── S3_test_R2_fastqc.html
│   │       └── S3_test_R2_fastqc.zip
│   └── MultiQC_stats
│       └── multiqc_report.html
├── QC_trimming
│   ├── Paired
│   │   ├── S1_test.1P.fastq.gz
│   │   ├── S1_test.2P.fastq.gz
│   │   ├── S2_test.1P.fastq.gz
│   │   ├── S2_test.2P.fastq.gz
│   │   ├── S3_test.1P.fastq.gz
│   │   └── S3_test.2P.fastq.gz
│   └── Unpaired
│       ├── S1_test.1U.fastq.gz
│       ├── S1_test.2U.fastq.gz
│       ├── S2_test.1U.fastq.gz
│       ├── S2_test.2U.fastq.gz
│       ├── S3_test.1U.fastq.gz
│       └── S3_test.2U.fastq.gz
├── ResistomeAnalysis
│   ├── Rarefaction
│   │   └── Counts
│   │       ├── S1_test.class.tsv
│   │       ├── S1_test.gene.tsv
│   │       ├── S1_test.group.tsv
│   │       ├── S1_test.mech.tsv
│   │       ├── S1_test.type.tsv
│   │       ├── S2_test.class.tsv
│   │       ├── S2_test.gene.tsv
│   │       ├── S2_test.group.tsv
│   │       ├── S2_test.mech.tsv
│   │       ├── S2_test.type.tsv
│   │       ├── S3_test.class.tsv
│   │       ├── S3_test.gene.tsv
│   │       ├── S3_test.group.tsv
│   │       ├── S3_test.mech.tsv
│   │       └── S3_test.type.tsv
│   └── ResistomeCounts
│       ├── S1_test.AMR.class.tsv
│       ├── S1_test.AMR.gene.tsv
│       ├── S1_test.AMR.group.tsv
│       ├── S1_test.AMR.mechanism.tsv
│       ├── S1_test.AMR.type.tsv
│       ├── S1_test.dedup_AMR.class.tsv
│       ├── S1_test.dedup_AMR.gene.tsv
│       ├── S1_test.dedup_AMR.group.tsv
│       ├── S1_test.dedup_AMR.mechanism.tsv
│       ├── S1_test.dedup_AMR.type.tsv
│       ├── S2_test.AMR.class.tsv
│       ├── S2_test.AMR.gene.tsv
│       ├── S2_test.AMR.group.tsv
│       ├── S2_test.AMR.mechanism.tsv
│       ├── S2_test.AMR.type.tsv
│       ├── S2_test.dedup_AMR.class.tsv
│       ├── S2_test.dedup_AMR.gene.tsv
│       ├── S2_test.dedup_AMR.group.tsv
│       ├── S2_test.dedup_AMR.mechanism.tsv
│       ├── S2_test.dedup_AMR.type.tsv
│       ├── S3_test.AMR.class.tsv
│       ├── S3_test.AMR.gene.tsv
│       ├── S3_test.AMR.group.tsv
│       ├── S3_test.AMR.mechanism.tsv
│       ├── S3_test.AMR.type.tsv
│       ├── S3_test.dedup_AMR.class.tsv
│       ├── S3_test.dedup_AMR.gene.tsv
│       ├── S3_test.dedup_AMR.group.tsv
│       ├── S3_test.dedup_AMR.mechanism.tsv
│       └── S3_test.dedup_AMR.type.tsv
└── Results
    ├── AMR_analytic_matrix.csv
    ├── SNPconfirmed_AMR_analytic_matrix.csv
    ├── SNPconfirmed_dedup_AMR_analytic_matrix.csv
    ├── Stats
    │   ├── host.removal.stats
    │   └── trimmomatic.stats
    └── dedup_AMR_analytic_matrix.csv