├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md ├── markdownlint.yml └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── push_dockerhub_dev.yml │ └── push_dockerhub_release.yml ├── .gitignore ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── Dockerfile ├── LICENSE ├── README.md ├── assets ├── adapters.fa ├── email_template.html ├── email_template.txt ├── multiqc_config.yaml ├── nf-core-dualrnaseq_logo.png └── sendmail_template.txt ├── bin ├── RNA_class_content.py ├── calculate_TPM_HTSeq.R ├── check_replicates.py ├── collect_quantification_data.py ├── collect_total_raw_read_pairs.py ├── combine_annotations_salmon_gene_level.py ├── combine_quant_annotations.py ├── combine_tables.py ├── count_cross_mapped_reads.sh ├── count_multi_mapped_read_pairs.sh ├── count_multi_mapped_reads.sh ├── count_total_reads.sh ├── count_uniquely_mapped_read_pairs.sh ├── count_uniquely_mapped_reads.sh ├── extract_annotations_from_gff.py ├── extract_crossmapped_reads.py ├── extract_processed_reads.sh ├── extract_reference_names_from_fasta_files.sh ├── gff_to_fasta_transcriptome.py ├── mapping_stats.py ├── markdown_to_html.py ├── plot_RNA_class_stats_combined.py ├── plot_RNA_class_stats_each.py ├── plot_mapping_statistics_salmon.py ├── plot_mapping_statistics_salmon_alignment.py ├── plot_mapping_stats_htseq.py ├── plot_mapping_stats_star.py ├── remove_crossmapped_read_pairs_BAM.sh ├── remove_crossmapped_reads_BAM.sh ├── replace_attribute_gff.sh ├── replace_feature_gff.sh ├── salmon_extract_ambig_uniq_transcripts_genes.R ├── salmon_host_comb_ambig_uniq.R ├── salmon_pathogen_comb_ambig_uniq.R ├── scatter_plots.py ├── scrape_software_versions.py ├── split_quant_tables.sh ├── split_quant_tables_salmon.sh └── tximport.R ├── conf ├── base.config ├── genomes.config ├── test.config └── test_full.config ├── data └── RNA_classes_to_replace.tsv ├── docs ├── README.md ├── images │ ├── RNA_class_stats_combined_host_htseq.png │ ├── RNA_class_stats_combined_host_salmon.png │ ├── RNA_class_stats_combined_host_salmon_al.png │ ├── RNA_class_stats_combined_pathogen_htseq.png │ ├── RNA_class_stats_combined_pathogen_salmon.png │ ├── RNA_class_stats_combined_pathogen_salmon_al.png │ ├── RNA_class_stats_sample_host_htseq.png │ ├── RNA_class_stats_sample_host_salmon.png │ ├── RNA_class_stats_sample_host_salmon_al.png │ ├── RNA_class_stats_sample_pathogen_htseq.png │ ├── RNA_class_stats_sample_pathogen_salmon.png │ ├── RNA_class_stats_sample_pathogen_salmon_al.png │ ├── Workflow_diagram_dualrnaseq.png │ ├── mapping_stats_samples_percentage_htseq.png │ ├── mapping_stats_samples_percentage_salmon.png │ ├── mapping_stats_samples_percentage_salmon_al.png │ ├── mapping_stats_samples_percentage_star.png │ ├── mapping_stats_samples_total_reads_htseq.png │ ├── mapping_stats_samples_total_reads_salmon.png │ ├── mapping_stats_samples_total_reads_salmon_al.png │ ├── mapping_stats_samples_total_reads_star.png │ ├── nf-core-dualrnaseq_logo.png │ ├── scatter_plot_host_HTseq.png │ ├── scatter_plot_host_salmon.png │ ├── scatter_plot_host_salmon_al.png │ ├── scatter_plot_pathogen_HTseq.png │ ├── scatter_plot_pathogen_salmon.png │ └── scatter_plot_pathogen_salmon_al.png ├── output.md ├── parameters.md └── usage.md ├── environment.yml ├── main.nf ├── nextflow.config └── nextflow_schema.json /.gitattributes: -------------------------------------------------------------------------------- 1 | *.config linguist-language=nextflow 2 | -------------------------------------------------------------------------------- /.github/.dockstore.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/dualrnaseq/HEAD/.github/.dockstore.yml 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