├── .devcontainer ├── devcontainer.json └── setup.sh ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml ├── python │ ├── find_changed_files.py │ └── include.yaml └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix_linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── nf-test.yml │ ├── release-announcements.yml │ └── template-version-comment.yml ├── .gitignore ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .vscode └── settings.json ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-riboseq_logo_light.png ├── rrna-db-defaults.txt ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── filter_gtf.py └── gtf2bed ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── test.config └── test_full.config ├── docs ├── README.md ├── images │ ├── fc.png │ ├── mqc_cutadapt_trimmed.png │ ├── mqc_fastp_plot.png │ ├── mqc_samtools_idxstats.png │ ├── mqc_samtools_mapped.png │ ├── mqc_sortmerna.png │ ├── mqc_star.png │ ├── nf-core-riboseq_logo.svg │ ├── nf-core-riboseq_logo_dark.png │ ├── nf-core-riboseq_logo_light.png │ ├── nf-core-riboseq_metro_map.png │ └── nf-core-riboseq_metro_map.svg ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── gtf2bed │ │ └── main.nf │ ├── gtf_filter │ │ └── main.nf │ ├── preprocess_transcripts_fasta_gencode │ │ └── main.nf │ └── star_genomegenerate_igenomes │ │ └── main.nf └── nf-core │ ├── anota2seq │ └── anota2seqrun │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── anota2seqrun.r │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bbmap │ └── bbsplit │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── cat │ └── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── custom │ ├── catadditionalfasta │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ │ └── fasta2gtf.py │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── getchromsizes │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── tx2gene │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── tx2gene.py │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── cutadapt │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── fastp │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.interleaved.config │ │ └── nextflow.save_failed.config │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── fq │ ├── lint │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── subsample │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── nextflow_no_args.config │ │ ├── nextflow_probability.config │ │ └── nextflow_record_count.config │ ├── gffread │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow-fasta.config │ │ ├── nextflow-gff3.config │ │ ├── nextflow.config │ │ └── tags.yml │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── kallisto │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── quant │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── ribotish │ ├── predict │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── quality │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── ribotricer │ ├── detectorfs │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.all.config │ │ │ ├── nextflow.filtered.config │ │ │ └── tags.yml │ └── prepareorfs │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── ribowaltz │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── templates │ │ └── ribowaltz.r │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── rsem │ └── preparereference │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── salmon │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── quant │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── samtools │ ├── flagstat │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── idxstats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow_cram.config │ │ │ └── tags.yml │ └── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── sortmerna │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── indexing_only.config │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── premade_index.config │ ├── star │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.arriba.config │ │ │ ├── nextflow.config │ │ │ ├── nextflow.starfusion.config │ │ │ └── tags.yml │ └── genomegenerate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── summarizedexperiment │ └── summarizedexperiment │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── summarizedexperiment.r │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── multi_matrix.config │ │ ├── single_matrix.config │ │ └── tags.yml │ ├── trimgalore │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── tximeta │ └── tximport │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── tximport.r │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── umicollapse │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── umitools │ ├── dedup │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── extract │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── prepareforrsem │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ └── untar │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── tags.yml ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── prepare_genome │ │ └── main.nf │ └── utils_nfcore_riboseq_pipeline │ │ └── main.nf └── nf-core │ ├── bam_dedup_stats_samtools_umicollapse │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── paired-end-umis.config │ │ └── tags.yml │ ├── bam_dedup_stats_samtools_umitools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bam_dedup_umi │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── bam_sort_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bam_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── fastq_align_star │ ├── main.nf │ ├── meta.yml │ ├── nextflow.config │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── tags.yml │ │ └── with_transcripts.config │ ├── fastq_fastqc_umitools_fastp │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── fastq_fastqc_umitools_trimgalore │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── fastq_qc_trim_filter_setstrandedness │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── fastq_subsample_fq_salmon │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── quantify_pseudo_alignment │ ├── main.nf │ ├── 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