├── .gitignore ├── Changelog.md ├── LICENSE ├── README.md ├── dockerfiles ├── finder │ └── 2.0.0 │ │ └── Dockerfile ├── repeatmasker │ └── 4.1.2 │ │ └── Dockerfile ├── samtools │ └── 1.16 │ │ └── Dockerfile ├── sratools │ └── 3.0.0 │ │ └── Dockerfile └── star │ └── 2.7.10a │ └── Dockerfile ├── example ├── Arabidopsis_thaliana_metadata.csv ├── raw_data │ ├── dummy_data1.fastq │ └── dummy_data2.fastq.gz └── uniprot_ARATH.fasta ├── finder ├── finder_old ├── mongodb_schema_design ├── README.md ├── collection-mrna_seq_short_read_samples.json └── collection-project_info.json ├── proposed_changes_for_version2.md ├── src ├── STAR_parameters │ ├── evolutionarily_close.json │ └── evolutionarily_distant.json ├── calculate_STAR_index_generation_parameters └── change_reference_ids ├── tests ├── align_with_star_multiple_rounds_PE.json ├── align_with_star_multiple_rounds_SE.json ├── finder │ └── arath │ │ └── metadata.csv └── test_commands ├── tools ├── finder │ └── 2.0.0 │ │ ├── calculate_star_index_generation_parameters.cwl │ │ └── change_reference_files.cwl ├── repeatmasker │ └── 4.1.2 │ │ ├── repeatmasker.cwl │ │ └── test ├── samtools │ └── 1.16.1 │ │ ├── samtools_faidx.cwl │ │ ├── samtools_fqidx.cwl │ │ ├── samtools_import.cwl │ │ ├── samtools_index.cwl │ │ ├── samtools_merge.cwl │ │ ├── samtools_sort.cwl │ │ └── samtools_view.cwl ├── sratools │ └── 3.0.0 │ │ ├── fasterq_dump.cwl │ │ └── prefetch.cwl └── star │ └── 2.7.10a │ ├── star_align.cwl │ └── star_generate_index.cwl └── workflows ├── align_with_star_multiple_rounds.cwl ├── download_from_sra_and_convert_to_fasta.cwl └── star_generate_index.cwl /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sagnikbanerjee15/Finder/HEAD/.gitignore -------------------------------------------------------------------------------- /Changelog.md: -------------------------------------------------------------------------------- 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