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4. Outputs and Report

Inês Mendes edited this page Jul 1, 2019 · 4 revisions
  • Output Results

After completion and as with any other Nextflow pipeline, the output files of all tools in DEN-IM are stored in the resultsin the directory where the workflow was executed. It includes the QC'ed read data, the read data after DENV filtering and the amount of sequences that mapped to the reference DENV sequences, the assembled sequences, the ORF sequences, the serotyping and genotyping results, the ORF alignment file and the phylogenetic tree file. The execution log file for each component, as well as a log file for the execution of the workflow, are also available.

For the dataset used in the How to run DEN-IM setion, these were the output files obtained:

$ tree results

results
├── alignment
│   └── mafft_1_12
│       └── DEN-IM.nf.align -> /home/ines/DEN-IM/DENIM/work/2b/a448a59c82d9c1e1fb4f7ec676bf0d/DEN-IM.nf.align
├── assembly
│   ├── megahit_1_7
│   │   └── SRR5821236_megahit113.fasta
│   ├── pilon_1_9
│   │   └── SRR5821236_megahit113_filt_polished.fasta
│   ├── spades_1_7
│   └── split_assembly_1_10
│       └── SRR5821236
│           └── SRR5821236_k77_1_flag_1_multi_12864.0000_len_10232_pilon.fasta -> /home/ines/DEN-IM/DEN-IM/work/85/4eba3ac5c34526d40bc5f675587cd2/SRR5821236_k77_1_flag_1_multi_12864.0000_len_10232_pilon.fasta
├── dengue_typing
│   └── SRR5821236_k77_1_flag_1_multi_12864.0000_len_10232_pilon
│       ├── gb:HQ705619.fa -> /home/ines/DEN-IM/DEN-IM/work/52/251ecf42d0090715770648643e2e36/gb:HQ705619.fa
│       ├── seq_typing.report.txt -> /home/ines/DEN-IM/DEN-IM/work/52/251ecf42d0090715770648643e2e36/seq_typing.report.txt
│       ├── seq_typing.report_types.tab -> /home/ines/DEN-IM/DEN-IM/work/52/251ecf42d0090715770648643e2e36/seq_typing.report_types.tab
│       └── SRR5821236_k77_1_flag_1_multi_12864.0000_len_10232_pilon.fasta -> /home/ines/DEN-IM/DEN-IM/work/52/251ecf42d0090715770648643e2e36/SRR5821236_k77_1_flag_1_multi_12864.0000_len_10232_pilon.fasta
├── mapping
│   ├── bowtie_1_4
│   │   ├── SRR5821236.bam -> /home/ines/DEN-IM/DEN-IM/work/54/c9e1ea61102b583e130d4d005f809a/SRR5821236.bam
│   │   └── SRR5821236_bowtie2.log -> /home/ines/DEN-IM/DEN-IM/work/54/c9e1ea61102b583e130d4d005f809a/SRR5821236_bowtie2.log
│   └── retrieve_mapped_1_5
│       ├── SRR5821236_mapped_1.headersRenamed_1.fq.gz -> /home/ines/DEN-IM/DEN-IM/work/0a/3625d778dea84c46c9709319b1f15e/SRR5821236_mapped_1.headersRenamed_1.fq.gz
│       └── SRR5821236_mapped_2.headersRenamed_2.fq.gz -> /home/ines/DEN-IM/DEN-IM/work/0a/3625d778dea84c46c9709319b1f15e/SRR5821236_mapped_2.headersRenamed_2.fq.gz
├── phylogeny
│   └── raxml_1_13
│       ├── RAxML_bestTree.DEN-IM.nf -> /home/ines/DEN-IM/DEN-IM/work/da/ab844928a9ab8b5a09be0e3a09b781/RAxML_bestTree.DEN-IM.nf
│       ├── RAxML_bipartitionsBranchLabels.DEN-IM.nf -> /home/ines/DEN-IM/DEN-IM/work/da/ab844928a9ab8b5a09be0e3a09b781/RAxML_bipartitionsBranchLabels.DEN-IM.nf
│       ├── RAxML_bipartitions.DEN-IM.nf -> /home/ines/DEN-IM/DEN-IM/work/da/ab844928a9ab8b5a09be0e3a09b781/RAxML_bipartitions.DEN-IM.nf
│       ├── RAxML_bootstrap.DEN-IM.nf -> /home/ines/DEN-IM/DEN-IM/work/da/ab844928a9ab8b5a09be0e3a09b781/RAxML_bootstrap.DEN-IM.nf
│       └── RAxML_info.DEN-IM.nf -> /home/ines/DEN-IM/DEN-IM/work/da/ab844928a9ab8b5a09be0e3a09b781/RAxML_info.DEN-IM.nf
└── trimmomatic_1_2
    ├── SRR5821236_1_trim.fastq.gz -> /home/ines/DEN-IM/DEN-IM/work/b1/27b64cbf7c425d75952f4b5da6b2d5/SRR5821236_1_trim.fastq.gz
    └── SRR5821236_2_trim.fastq.gz -> /home/ines/DEN-IM/DEN-IM/work/b1/27b64cbf7c425d75952f4b5da6b2d5/SRR5821236_2_trim.fastq.gz

16 directories, 19 files

The heavier files are stored as symlinks to their original location inside the work/ directory, but this behavior can be altered by adding the following code to the user.config file.

  • Report

DEN-IM creates an interactive HTML report, stored in the pipeline_results folder in the directory where the workflow was executed. It contains all the information in the results divided into 4 sections: report overview, tables, charts and phylogenetic tree. To open the report simply click oh the pipeline_report.html file and the report will open on your default browser. To share the report with someone, zip the entire pipeline_results folder as the pipeline_report.html file won't function without the files inside src directory included here.

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