├── .gitattributes ├── .gitignore ├── .gitmodules ├── .travis.yml ├── CHANGELOG.md ├── Dockerfile ├── LICENSE ├── NF+LSF.txt ├── README.md ├── TODO ├── assets ├── biotypes_header.txt ├── heatmap_header.txt └── mdsplot_header.txt ├── bin ├── dupRadar.r ├── edgeR_heatmap_MDS.r ├── gtf2bed ├── irods.sh ├── markdown_to_html.r ├── merge-files-col.sh ├── merge_featurecounts.py ├── mito.py └── mqc_features_stat.py ├── conf ├── aws.config ├── base.config ├── farm3.config ├── farm4.config ├── genomes.config ├── images.config ├── lsf.config ├── monoconda.config ├── multiqc_config.yaml ├── singularity.config └── soloconda.config ├── docs ├── README.md ├── Troubleshooting.md ├── amazon_web_services.md ├── images │ ├── NGI-RNAseq_logo.ai │ ├── NGI-RNAseq_logo.eps │ ├── NGI-RNAseq_logo.pdf │ ├── NGI-RNAseq_logo.png │ ├── NGI-RNAseq_logo.svg │ ├── NGI_logo.png │ ├── SciLifeLab_logo.png │ ├── cutadapt_plot.png │ ├── dupRadar_plot.png │ ├── featureCounts_assignment_plot.png │ ├── featureCounts_biotype_plot.png │ ├── heatmap.png │ ├── infer_experiment.png │ ├── inner_distance_concept.png │ ├── junction_saturation.png │ ├── mqc_hcplot_hocmzpdjsq.png │ ├── mqc_hcplot_ltqchiyxfz.png │ ├── mqc_hcplot_wtnqrdhkuc.png │ ├── preseq_complexity_curve.png │ ├── preseq_plot.png │ ├── read_duplication.png │ ├── rseqc_gene_body_coverage_plot.png │ ├── rseqc_infer_experiment_plot.png │ ├── rseqc_inner_distance_plot.png │ ├── rseqc_junction_annotation_junctions_plot.png │ ├── rseqc_junction_saturation_plot.png │ ├── rseqc_read_distribution_plot.png │ ├── rseqc_read_dups_plot.png │ ├── saturation.png │ └── star_alignment_plot.png ├── installation.md ├── output.md └── usage.md ├── env-rnaseq1.6.yml ├── env-rnaseq1.7.yml ├── environment.yml ├── flowchart.png ├── main.nf ├── nextflow.config └── tests ├── amazon_test.sh ├── docker_test.sh └── docker_test_hisat.sh /.gitattributes: -------------------------------------------------------------------------------- 1 | *.nf 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