A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/reportho analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2024-07-18, 13:31 UTC
based on data in:
/fusion/s3/nf-core-awsmegatests/work/reportho/work-42b305199b903365b71e7a8554cfcc6a822da8a8/9f/d42634a1dcd5496fc94a36aa834586
Software Versions
Software Versions lists versions of software tools extracted from file contents.
Group | Software | Version |
---|---|---|
CONVERT_FASTA | Biopython | 1.83 |
Python | 3.11.0 | |
CONVERT_PHYLIP | Biopython | 1.83 |
Python | 3.11.0 | |
FASTME | fastme | 2.1.6.1 |
FETCH_AFDB_STRUCTURES | Python | 3.11.0 |
Python Requests | 2.31.0 | |
FETCH_INSPECTOR_GROUP_ONLINE | OrthoInspector Database | Eukaryota2023 |
Python | 3.11.0 | |
Python Requests | 2.31.0 | |
FETCH_OMA_GROUP_ONLINE | OMA API | 1.1 |
OMA Database | All.Jul2023 | |
Python | 3.11.0 | |
Python Requests | 2.31.0 | |
FETCH_PANTHER_GROUP_ONLINE | Panther Database | null |
Python | 3.11.0 | |
Python Requests | 2.31.0 | |
FETCH_SEQUENCES_ONLINE | OMA API | 1.1 |
OMA Database | All.Jul2023 | |
Python | 3.11.0 | |
Python Requests | 2.31.0 | |
FILTER_FASTA | Python | 3.11.0 |
FILTER_HITS | Python | 3.11.0 |
IQTREE | iqtree | 2.3.0 |
MAKE_HITS_TABLE | Python | 3.11.0 |
MAKE_REPORT | Node | 22.1.0 |
React | 18.3.1 | |
Yarn | 1.22.19 | |
MAKE_SCORE_TABLE | Python | 3.11.0 |
MAKE_STATS | Python | 3.11.0 |
MERGE_CSV | csvtk | 0.30.0 |
MERGE_HITS | csvtk | 0.30.0 |
MERGE_STATS | csvtk | 0.30.0 |
PLOT_FASTME | r-base | 4.3.3 |
PLOT_IQTREE | r-base | 4.3.3 |
PLOT_ORTHOLOGS | r-base | 4.3.3 |
STATS2CSV | PyYAML | 5.4.1 |
Python | 3.9.6 | |
TCOFFEE_3DALIGN | pigz | 2.8) |
tcoffee | 13.46.0.919e8c6b | |
WRITE_SEQINFO | Python | 3.11.0 |
Python Requests | 2.31.0 | |
Workflow | Nextflow | 23.10.1 |
nf-core/reportho | v1.0.1-g42b3051 |
nf-core/reportho Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.
Methods
Data was processed using nf-core/reportho v1.0.1 (doi: 10.5281/zenodo.11574565) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v23.10.1 (Di Tommaso et al., 2017) with the following command:
nextflow run 'https://github.com/nf-core/reportho' -name maniac_descartes -params-file 'https://api.cloud.seqera.io/ephemeral/Rv-kRNA4a0DIx2JlNYi5Bw.json' -with-tower -r 42b305199b903365b71e7a8554cfcc6a822da8a8 -profile test_full
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/reportho Workflow Summary
- this information is collected when the pipeline is started.
Core Nextflow options
- revision
- 1.0.1
- runName
- maniac_descartes
- launchDir
- /
- workDir
- /nf-core-awsmegatests/work/reportho/work-42b305199b903365b71e7a8554cfcc6a822da8a8
- projectDir
- /.nextflow/assets/nf-core/reportho
- userName
- root
- profile
- test_full
- configFiles
- N/A
Input/output options
- input
- https://raw.githubusercontent.com/nf-core/test-datasets/reportho/testdata/samplesheet/samplesheet.csv
- outdir
- s3://nf-core-awsmegatests/reportho/results-42b305199b903365b71e7a8554cfcc6a822da8a8
Ortholog search options
- eggnog_path
- http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/1/1_members.tsv.gz
- eggnog_idmap_path
- http://eggnog5.embl.de/download/eggnog_5.0/id_mappings/uniprot/latest.Eukaryota.tsv.gz
- min_score
- 3
Downstream analysis options
- use_structures
- true
Institutional config options
- config_profile_name
- Full test profile
- config_profile_description
- Full test dataset to check pipeline function
Generic options
- hook_url
- https://hooks.slack.com/services/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