├── .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 ├── .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 ├── bamtools_filter_pe.json ├── bamtools_filter_se.json ├── blacklists │ ├── v1.0 │ │ ├── GRCh37-blacklist.v1.bed │ │ └── hg19-blacklist.v1.bed │ ├── v2.0 │ │ ├── GRCm38-blacklist.v2.bed │ │ ├── ce10-blacklist.v2.bed │ │ ├── ce11-blacklist.v2.bed │ │ ├── dm3-blacklist.v2.bed │ │ ├── dm6-blacklist.v2.bed │ │ ├── hg19-blacklist.v2.bed │ │ ├── hg38-blacklist.v2.bed │ │ └── mm10-blacklist.v2.bed │ └── v3.0 │ │ ├── GRCh38-blacklist.v3.bed │ │ └── hg38-blacklist.v3.bed ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc │ ├── deseq2_clustering_header.txt │ ├── deseq2_pca_header.txt │ ├── frip_score_header.txt │ ├── peak_annotation_header.txt │ ├── peak_count_header.txt │ ├── spp_correlation_header.txt │ ├── spp_nsc_header.txt │ └── spp_rsc_header.txt ├── multiqc_config.yml ├── nf-core-chipseq_logo_light.png ├── samplesheet_pe.csv ├── samplesheet_se.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── bampe_rm_orphan.py ├── check_samplesheet.py ├── deseq2_qc.r ├── gtf2bed ├── igv_files_to_session.py ├── macs3_merged_expand.py ├── plot_homer_annotatepeaks.r ├── plot_macs3_qc.r └── plot_peak_intersect.r ├── conf ├── base.config ├── igenomes.config ├── modules.config ├── test.config └── test_full.config ├── docs ├── README.md ├── images │ ├── igv_screenshot.png │ ├── mqc_annotatePeaks_feature_percentage_plot.png │ ├── mqc_cutadapt_plot.png │ ├── mqc_deeptools_plotFingerprint_plot.png │ ├── mqc_deeptools_plotProfile_plot.png │ ├── mqc_deseq2_pca_plot.png │ ├── mqc_deseq2_sample_similarity_plot.png │ ├── mqc_fastqc_adapter.png │ ├── mqc_fastqc_counts.png │ ├── mqc_fastqc_quality.png │ ├── mqc_featureCounts_assignment_plot.png │ ├── mqc_frip_score_plot.png │ ├── mqc_macs3_peak_count_plot.png │ ├── mqc_picard_deduplication_plot.png │ ├── mqc_picard_insert_size_plot.png │ ├── mqc_preseq_plot.png │ ├── mqc_samtools_stats_plot.png │ ├── mqc_spp_nsc_plot.png │ ├── mqc_spp_rsc_plot.png │ ├── mqc_spp_strand_correlation_plot.png │ ├── nf-core-chipseq_logo_dark.png │ ├── nf-core-chipseq_logo_light.png │ ├── nf-core-chipseq_metro_map_grey.png │ ├── nf-core-chipseq_metro_map_grey.svg │ └── r_upsetr_intersect_plot.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── annotate_boolean_peaks.nf │ ├── bam_remove_orphans.nf │ ├── bamtools_filter.nf │ ├── bedtools_genomecov.nf │ ├── deseq2_qc.nf │ ├── frip_score.nf │ ├── genome_blacklist_regions.nf │ ├── gtf2bed.nf │ ├── igv.nf │ ├── macs3_consensus.nf │ ├── multiqc.nf │ ├── multiqc_custom_peaks.nf │ ├── multiqc_custom_phantompeakqualtools.nf │ ├── plot_homer_annotatepeaks.nf │ ├── plot_macs3_qc.nf │ ├── samplesheet_check.nf │ ├── star_align.nf │ └── star_genomegenerate.nf └── nf-core │ ├── 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 │ ├── bwa │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── mem │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── chromap │ ├── chromap │ │ ├── chromap-chromap.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── custom │ └── getchromsizes │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── deeptools │ ├── computematrix │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── plotfingerprint │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── plotheatmap │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── plotprofile │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── 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 │ ├── homer │ └── annotatepeaks │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── khmer │ └── uniquekmers │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── macs3 │ └── callpeak │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── bam.config │ │ ├── bed.config │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── phantompeakqualtools │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── picard │ ├── collectmultiplemetrics │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── markduplicates │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── mergesamfiles │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── preseq │ └── lcextrap │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── 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 │ ├── subread │ └── featurecounts │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── trimgalore │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── ucsc │ └── bedgraphtobigwig │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── 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 │ └── untarfiles │ ├── environment.yml │ ├── main.nf │ └── meta.yml ├── nextflow.config ├── nextflow_schema.json ├── subworkflows ├── local │ ├── align_star.nf │ ├── bam_bedgraph_bigwig_bedtools_ucsc.nf │ ├── bam_filter_bamtools.nf │ ├── bam_peaks_call_qc_annotate_macs3_homer.nf │ ├── bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf │ ├── input_check.nf │ ├── prepare_genome.nf │ └── utils_nfcore_chipseq_pipeline │ │ └── main.nf └── nf-core │ ├── bam_markduplicates_picard │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── 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_bowtie2 │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── fastq_align_bwa │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── fastq_align_chromap │ ├── main.nf │ └── meta.yml │ ├── fastq_fastqc_umitools_trimgalore │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── 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 │ │ ├── main.workflow.nf.test │ │ ├── main.workflow.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ └── utils_nfvalidation_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow_schema.json │ └── tags.yml ├── tower.yml └── workflows └── chipseq.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- 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