├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── labeler.yml ├── release.yml └── workflows │ ├── ci.yml │ ├── deploy.yml │ ├── docs.yml │ └── label_prs.yml ├── .gitignore ├── .snakemake-workflow-catalog.yml ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── PULL_REQUEST_TEMPLATE.md ├── README.md ├── config ├── PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE ├── README.md └── config.yaml ├── docs ├── README.md ├── guides │ ├── images │ │ ├── bioconda_cutadapt.png │ │ ├── biocontainers_cutadapt.png │ │ ├── zarp_multiqc.png │ │ ├── zarp_multiqc_alfa_biotypes.png │ │ ├── zarp_multiqc_alfa_categories.png │ │ ├── zarp_multiqc_cutadapt_filtered_reads_plot.png │ │ ├── zarp_multiqc_fastqc_per_base_sequence_quality_plot.png │ │ ├── zarp_multiqc_fastqc_per_sequence_gc_content_plot.png │ │ ├── zarp_multiqc_fastqc_sequence_counts_plot.png │ │ ├── zarp_multiqc_general_statistics.png │ │ ├── zarp_multiqc_kallisto_alignment.png │ │ ├── zarp_multiqc_salmon_plot.png │ │ ├── zarp_multiqc_star_alignment_plot.png │ │ ├── zarp_multiqc_tin_score.png │ │ └── zarp_multiqc_zpca.png │ ├── installation.md │ ├── outputs.md │ ├── parameterization.md │ └── usage.md ├── images │ ├── biozentrum_logo.200px.png │ ├── poster_ZARP_latest.jpg │ ├── sib_logo.200px.png │ ├── zarp_logo.256px.png │ ├── zarp_logo.32px.png │ ├── zarp_logo.384px.png │ └── zavolab_logo.200px.png ├── includes │ ├── abbreviations.md │ └── references.md ├── overrides │ └── .icons │ │ ├── email.svg │ │ ├── forum.svg │ │ ├── github.svg │ │ └── twitter.svg └── requirements.txt ├── images ├── dag_test_workflow.svg ├── logo.128px.png ├── zarp_logo.svg └── zarp_schema.png ├── install ├── environment.dev.yml └── environment.yml ├── mkdocs.yml ├── pipeline_documentation.md ├── profiles ├── CookieCutterSlurm.py ├── graphs │ └── config.yaml ├── local-apptainer │ └── config.yaml ├── local-conda │ └── config.yaml ├── slurm-apptainer │ └── config.yaml ├── slurm-conda │ └── config.yaml ├── slurm-config.json ├── slurm-jobscript.sh ├── slurm-settings.json ├── slurm-sidecar.py ├── slurm-status.py ├── slurm-submit.py └── slurm_utils.py ├── resources └── config_schema.json ├── tests ├── input_files │ ├── config.mutliple_lanes.yml │ ├── config.yaml │ ├── config_alfa.yaml │ ├── config_docker.yaml │ ├── homo_sapiens │ │ ├── annotation.gtf │ │ ├── genome.fa │ │ ├── quick_start.gtf │ │ └── transcriptome.fa │ ├── htsinfer_samples.tsv │ ├── pe_lane1 │ │ ├── synthetic_split_lane1.mate_1.fastq.gz │ │ └── synthetic_split_lane1.mate_2.fastq.gz │ ├── pe_lane2 │ │ ├── synthetic_split_lane2.mate_1.fastq.gz │ │ └── synthetic_split_lane2.mate_2.fastq.gz │ ├── project1 │ │ ├── synthetic.mate_1.fastq.gz │ │ └── synthetic.mate_2.fastq.gz │ ├── project2 │ │ └── synthetic.mate_1.fastq.gz │ ├── rule_config.yaml │ ├── samples.multiple_lanes.tsv │ ├── samples.tsv │ ├── samples_alfa.tsv │ ├── samples_docker.tsv │ ├── se_lane1 │ │ └── synthetic_split_lane1.mate_1.fastq.gz │ ├── se_lane2 │ │ └── synthetic_split_lane2.mate_1.fastq.gz │ ├── sra_samples.tsv │ ├── synthetic.mate_1.bed │ ├── synthetic.mate_2.bed │ ├── testpath1.1.fastq │ ├── testpath1.2.fastq │ └── testpath2.1.fastq ├── test_create_dag_image │ └── test.sh ├── test_create_rule_graph │ └── test.sh ├── test_format │ ├── test_snakefmt.sh │ └── test_snakemake_lint.sh ├── test_htsinfer_with_apptainer │ ├── expected_output.md5 │ └── test.local.sh ├── test_htsinfer_with_conda │ ├── expected_output.md5 │ └── test.local.sh ├── test_integration_workflow │ ├── expected_output.files │ ├── expected_output.md5 │ ├── expected_output_temp_flag.files │ ├── expected_output_temp_flag.md5 │ ├── test.local.sh │ ├── test.slurm.sh │ └── test.temp.flag.sh ├── test_integration_workflow_multiple_lanes │ ├── expected_output.md5 │ ├── test.local.sh │ └── test.slurm.sh ├── test_integration_workflow_with_conda │ ├── expected_output.files │ ├── expected_output.md5 │ ├── test.local.sh │ └── test.slurm.sh ├── test_integration_workflow_with_docker │ └── test.local.sh ├── test_sra_download_with_apptainer │ ├── expected_output.files │ ├── expected_output.md5 │ ├── test.local.sh │ └── test.slurm.sh └── test_sra_download_with_conda │ ├── expected_output.files │ ├── expected_output.md5 │ ├── test.local.sh │ └── test.slurm.sh └── workflow ├── Snakefile ├── envs ├── STAR.yaml ├── alfa.yaml ├── bedtools.yaml ├── cutadapt.yaml ├── entrez-direct.yaml ├── fastqc.yaml ├── gffread.yaml ├── htsinfer.yaml ├── kallisto.yaml ├── pigz.yaml ├── r-merge-kallisto.yaml ├── salmon.yaml ├── samtools.yaml ├── sra-tools.yaml ├── tin-score-calculation.yaml ├── ucsc-bedgraphtobigwig.yaml ├── zavolan-multiqc-plugins.yaml ├── zgtf.yaml └── zpca.yaml ├── rules ├── common.smk ├── htsinfer.smk ├── paired_end.snakefile.smk ├── single_end.snakefile.smk ├── sra_download.smk ├── sra_paired_end.smk └── sra_single_end.smk └── scripts ├── htsinfer_to_tsv.py └── zarp_multiqc_config.py /.github/ISSUE_TEMPLATE/bug_report.md: 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