├── .devcontainer └── devcontainer.json ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix-linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── release-announcements.yml │ └── template_version_comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── email_template.html ├── email_template.txt ├── known_adapters.fa ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-smrnaseq_logo_light.png ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt ├── slackreport.json └── smrnaseq_logo.png ├── bin ├── collapse_mirtop.r └── edgeR_miRBase.r ├── conf ├── base.config ├── ci.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── protocol_cats.config ├── protocol_illumina.config ├── protocol_nextflex.config ├── protocol_qiaseq.config ├── test.config ├── test_contamination.config ├── test_contamination_tech_reps.config ├── test_full.config ├── test_full_filter_contamination.config ├── test_mirgenedb.config ├── test_nextflex.config ├── test_skipfastp.config ├── test_technical_repeats.config └── test_umi.config ├── docs ├── README.md ├── images │ ├── Example_MDS_plot.png │ ├── Example_heatmap.png │ ├── mirtrace_plot.png │ ├── nf-core-smrnaseq_logo_dark.png │ ├── nf-core-smrnaseq_logo_light.png │ ├── samtools_alignment_plot.png │ ├── smrnaseq_logo.ai │ └── smrnaseq_logo.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── datatable_merge │ │ ├── main.nf │ │ └── tests │ │ │ ├── datatable_merge.nf.test │ │ │ └── datatable_merge.nf.test.snap │ ├── edger_qc │ │ ├── main.nf │ │ └── tests │ │ │ ├── edger_qc.nf.test │ │ │ └── edger_qc.nf.test.snap │ ├── filter_stats.nf │ ├── format_fasta_mirna.nf │ └── parse_fasta_mirna.nf └── nf-core │ ├── bioawk │ ├── bioawk.diff │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── blat │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── bowtie │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── build │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bowtie2 │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── cram_crai.config │ │ │ ├── large_index.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── sam.config │ │ │ ├── sam2.config │ │ │ └── tags.yml │ └── build │ │ ├── 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 │ ├── csvtk │ └── join │ │ ├── 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 │ │ └── tags.yml │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── gawk │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── nextflow_with_program_file.config │ │ └── tags.yml │ ├── mirdeep2 │ ├── mapper │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── mirdeep2 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── mirtop │ ├── counts │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── export │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── gff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── mirtrace │ └── qc │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── multiqc │ ├── 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 │ ├── seqcluster │ └── collapse │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── seqkit │ ├── fq2fa │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── grep │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── seqkit-grep.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── replace │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── replace.config │ │ ├── tags.yml │ │ └── uncomp.config │ ├── umicollapse │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── nextflow_PE.config │ │ ├── nextflow_SE.config │ │ └── tags.yml │ ├── umitools │ └── extract │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── 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 ├── subworkflows ├── local │ ├── contaminant_filter │ │ ├── main.nf │ │ └── tests │ │ │ ├── contaminant_filter.nf.test │ │ │ └── nextflow.config │ ├── genome_quant.nf │ ├── mirna_quant.nf │ ├── prepare_genome │ │ └── main.nf │ └── utils_nfcore_smrnaseq_pipeline │ │ └── main.nf └── nf-core │ ├── bam_sort_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bam_stats_mirna_mirtop │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── bam_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── fastq_fastqc_umitools_fastp │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── nextflow.save_trimmed.config │ │ └── tags.yml │ ├── fastq_find_mirna_mirdeep2 │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── nextflow.config │ │ └── tags.yml │ ├── utils_nfcore_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── 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