From 6935743cd35aaaf7b67d648ababce77b5159ffca Mon Sep 17 00:00:00 2001 From: "Vishal Koparde, PhD" Date: Thu, 28 May 2026 12:55:09 -0400 Subject: [PATCH 1/2] docs(profile): expand pipeline descriptions and clean legend text Add a Description column with richer, pipeline-specific summaries in the profile README sources and rendered markdown. Simplify superscript legend entries to acronym expansions only, and remove generic placeholder wording from pipeline descriptions. _commit message is ai-generated_ --- profile/README.md | 38 +++++++++++++++++--------------------- profile/README.qmd | 34 +++++++++++++++++----------------- 2 files changed, 34 insertions(+), 38 deletions(-) diff --git a/profile/README.md b/profile/README.md index 4ee8525..9291c23 100644 --- a/profile/README.md +++ b/profile/README.md @@ -132,27 +132,26 @@ CCBR offers end-to-end analysis pipelines for NGS data analysis. Here is a list of our prominent pipelines and their release schedule on BIOWULF: -| Data Type | Pipeline Name | CLI\* available since | -| ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------- | -| RNASeq1 | [RENEE](https://github.com/CCBR/RENEE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | July 3rd 2023 | -| WESSeq2 | [XAVIER](https://github.com/CCBR/XAVIER)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | July 21st 2023 | -| ATACSeq3 | [ASPEN](https://github.com/CCBR/ASPEN)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | November 30th 2023 | -| ChIPSeq4 | [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | October 15th 2023 | -| CRISPRSeq5 | [CRISPIN](https://github.com/CCBR/CRISPIN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | September 2023 | -| CUT&RunSeq6 | [CARLISLE](https://github.com/CCBR/CARLISLE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | October 31st 2023 | -| EV-Seq10 | [ESCAPE](https://github.com/CCBR/ESCAPE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | March 26th 2024 | -| circRNASeq7 | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | September 16th 2024 | -| scRNASeq8 | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | February 28th 2025 | -| WGSSeq9 | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | May 31st 2025 | -| spatialSeq11 | [SPENCER](https://github.com/CCBR/SPENCER)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | TBD | +| Data Type | Pipeline Name | Description | CLI\* available since | +| ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------- | ----------- | -------------------------------- | +| RNASeq1 | [RENEE](https://github.com/CCBR/RENEE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Comprehensive RNA-seq workflow that combines contamination screening, adapter trimming, two-pass STAR alignment, and RSEM quantification. It generates gene and isoform count matrices, fusion calls, and MultiQC-style quality summaries for cohort-level review. | July 3rd 2023 | +| WESSeq2 | [XAVIER](https://github.com/CCBR/XAVIER)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Whole-exome sequencing pipeline aligned to Broad-style best practices using a reproducible Snakemake execution model. It accepts FASTQ or BAM inputs and supports germline and somatic variant calling, CNV inference, and downstream annotation. | July 21st 2023 | +| ATACSeq3 | [ASPEN](https://github.com/CCBR/ASPEN)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | ATAC-seq analysis workflow for preliminary QC, peak calling, and differential chromatin accessibility testing. It is configured for Biowulf usage and provides standardized outputs for regulatory genomics interpretation. | November 30th 2023 | +| ChIPSeq4 | [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | ChIP-seq analysis pipeline with support for configurable reference genomes and optional spike-in genome handling. It produces reproducible peak-centric outputs from aligned sequencing data and can be run through CCBR module-based workflows. | October 15th 2023 | +| CRISPRSeq5 | [CRISPIN](https://github.com/CCBR/CRISPIN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | CRISPR screen sequencing workflow designed for reproducible run setup and execution on Biowulf. It processes screening libraries into analysis-ready outputs suitable for guide-level and gene-level interpretation. | September 2023 | +| CUT&RunSeq6 | [CARLISLE](https://github.com/CCBR/CARLISLE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | CUT&RUN pipeline that performs peak calling with MACS2, SEACR, and GoPeaks using spike-in-normalized FASTQ inputs. It is built in Snakemake and tuned for reproducible chromatin profiling on Biowulf. | October 31st 2023 | +| EV-Seq10 | [ESCAPE](https://github.com/CCBR/ESCAPE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Extracellular vesicle RNA-seq workflow for EV-derived libraries from raw reads through analysis-ready quantification outputs. It emphasizes consistent QC and standardized processing for comparative EV transcriptomics. | March 26th 2024 | +| circRNASeq7 | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | circRNA pipeline for detection, annotation, and quantification of host and viral circular RNAs. It orchestrates multiple circRNA callers in parallel, including CIRCExplorer2 and CIRI2-based paths, to support robust cross-method discovery. | September 16th 2024 | +| scRNASeq8 | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Single-cell analysis resource supporting multiple next-generation modalities in a reproducible Nextflow framework. It starts from FASTQ or h5-aligned inputs, performs per-sample QC, and generates per-contrast integration reports. | February 28th 2025 | +| WGSSeq9 | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Whole-genome sequencing pipeline based on Broad-aligned processing patterns and Nextflow orchestration. It calls and annotates germline and somatic variants, CNVs, and SVs with reproducible containerized execution. | May 31st 2025 | +| spatialSeq11 | [SPENCER](https://github.com/CCBR/SPENCER)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Spatial sequencing workflow for processing location-aware transcriptomic measurements across tissue regions. It is designed to produce structured outputs for downstream spatial feature analysis, integration, and visualization. | TBD | \* CLI = Command Line Interface > ℹ️ GUI (Graphical User Interface) development has been suspended for > the time being but may resume in the future. - **1** RENEE=_Rna sEquencing aNalysis pipElinE_. Starts with raw -fastq files and ends with a counts matrix. + **1** RENEE=_Rna sEquencing aNalysis pipElinE_. **2** XAVIER=_eXome Analysis and Variant explorER_. @@ -161,14 +160,11 @@ fastq files and ends with a counts matrix. **4** CHAMPAGNE=_CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline_. - **5** CRISPIN=_CRISPr screen sequencing analysis pipelINe_. -CRISPRSeq analysis with MAGeCK, drugZ and BAGEL2. + **5** CRISPIN=_CRISPr screen sequencing analysis pipelINe_. - **6** CARLISLE=_Cut And Run anaLysIS pipeLinE_. Supports human and -mouse samples with (recommended) or without spike-ins. + **6** CARLISLE=_Cut And Run anaLysIS pipeLinE_. - **7** CHARLIE=_Circrnas in Host And viRuses anaLysis pIpEline_. -Finds known and novel circRNAs in human/mouse + virus genomes. + **7** CHARLIE=_Circrnas in Host And viRuses anaLysis pIpEline_. **8** SINCLAIR=_SINgle CelL AnalysIs Resource_. diff --git a/profile/README.qmd b/profile/README.qmd index 3fc02da..aa2e359 100644 --- a/profile/README.qmd +++ b/profile/README.qmd @@ -89,25 +89,25 @@ CCBR offers end-to-end analysis pipelines for NGS data analysis. Here is a list of our prominent pipelines and their release schedule on BIOWULF: -| Data Type | Pipeline Name | CLI\* available since | -| ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------- | -| RNASeq1 | [RENEE](https://github.com/CCBR/RENEE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | July 3rd 2023 | -| WESSeq2 | [XAVIER](https://github.com/CCBR/XAVIER)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | July 21st 2023 | -| ATACSeq3 | [ASPEN](https://github.com/CCBR/ASPEN)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | November 30th 2023 | -| ChIPSeq4 | [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | October 15th 2023 | -| CRISPRSeq5 | [CRISPIN](https://github.com/CCBR/CRISPIN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | September 2023 | -| CUT&RunSeq6 | [CARLISLE](https://github.com/CCBR/CARLISLE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | October 31st 2023 | -| EV-Seq10 | [ESCAPE](https://github.com/CCBR/ESCAPE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | March 26th 2024 | -| circRNASeq7 | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | September 16th 2024 | -| scRNASeq8 | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | February 28th 2025 | -| WGSSeq9 | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | May 31st 2025 | -| spatialSeq11 | [SPENCER](https://github.com/CCBR/SPENCER)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | TBD | +| Data Type | Pipeline Name | Description | CLI\* available since | +| ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------- | ----------- | --------------------------------- | +| RNASeq1 | [RENEE](https://github.com/CCBR/RENEE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Comprehensive RNA-seq workflow that combines contamination screening, adapter trimming, two-pass STAR alignment, and RSEM quantification. It generates gene and isoform count matrices, fusion calls, and MultiQC-style quality summaries for cohort-level review. | July 3rd 2023 | +| WESSeq2 | [XAVIER](https://github.com/CCBR/XAVIER)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Whole-exome sequencing pipeline aligned to Broad-style best practices using a reproducible Snakemake execution model. It accepts FASTQ or BAM inputs and supports germline and somatic variant calling, CNV inference, and downstream annotation. | July 21st 2023 | +| ATACSeq3 | [ASPEN](https://github.com/CCBR/ASPEN)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | ATAC-seq analysis workflow for preliminary QC, peak calling, and differential chromatin accessibility testing. It is configured for Biowulf usage and provides standardized outputs for regulatory genomics interpretation. | November 30th 2023 | +| ChIPSeq4 | [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | ChIP-seq analysis pipeline with support for configurable reference genomes and optional spike-in genome handling. It produces reproducible peak-centric outputs from aligned sequencing data and can be run through CCBR module-based workflows. | October 15th 2023 | +| CRISPRSeq5 | [CRISPIN](https://github.com/CCBR/CRISPIN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | CRISPR screen sequencing workflow designed for reproducible run setup and execution on Biowulf. It processes screening libraries into analysis-ready outputs suitable for guide-level and gene-level interpretation. | September 2023 | +| CUT&RunSeq6 | [CARLISLE](https://github.com/CCBR/CARLISLE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | CUT&RUN pipeline that performs peak calling with MACS2, SEACR, and GoPeaks using spike-in-normalized FASTQ inputs. It is built in Snakemake and tuned for reproducible chromatin profiling on Biowulf. | October 31st 2023 | +| EV-Seq10 | [ESCAPE](https://github.com/CCBR/ESCAPE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Extracellular vesicle RNA-seq workflow for EV-derived libraries from raw reads through analysis-ready quantification outputs. It emphasizes consistent QC and standardized processing for comparative EV transcriptomics. | March 26th 2024 | +| circRNASeq7 | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | circRNA pipeline for detection, annotation, and quantification of host and viral circular RNAs. It orchestrates multiple circRNA callers in parallel, including CIRCExplorer2 and CIRI2-based paths, to support robust cross-method discovery. | September 16th 2024 | +| scRNASeq8 | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Single-cell analysis resource supporting multiple next-generation modalities in a reproducible Nextflow framework. It starts from FASTQ or h5-aligned inputs, performs per-sample QC, and generates per-contrast integration reports. | February 28th 2025 | +| WGSSeq9 | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Whole-genome sequencing pipeline based on Broad-aligned processing patterns and Nextflow orchestration. It calls and annotates germline and somatic variants, CNVs, and SVs with reproducible containerized execution. | May 31st 2025 | +| spatialSeq11 | [SPENCER](https://github.com/CCBR/SPENCER)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Spatial sequencing workflow for processing location-aware transcriptomic measurements across tissue regions. It is designed to produce structured outputs for downstream spatial feature analysis, integration, and visualization. | TBD | \* CLI = Command Line Interface > ℹ️ GUI (Graphical User Interface) development has been suspended for the time being but may resume in the future. - **1** RENEE=_Rna sEquencing aNalysis pipElinE_. Starts with raw fastq files and ends with a counts matrix. + **1** RENEE=_Rna sEquencing aNalysis pipElinE_. **2** XAVIER=_eXome Analysis and Variant explorER_. @@ -115,11 +115,11 @@ Here is a list of our prominent pipelines and their release schedule on BIOWULF: **4** CHAMPAGNE=_CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline_. - **5** CRISPIN=_CRISPr screen sequencing analysis pipelINe_. CRISPRSeq analysis with MAGeCK, drugZ and BAGEL2. + **5** CRISPIN=_CRISPr screen sequencing analysis pipelINe_. - **6** CARLISLE=_Cut And Run anaLysIS pipeLinE_. Supports human and mouse samples with (recommended) or without spike-ins. + **6** CARLISLE=_Cut And Run anaLysIS pipeLinE_. - **7** CHARLIE=_Circrnas in Host And viRuses anaLysis pIpEline_. Finds known and novel circRNAs in human/mouse + virus genomes. + **7** CHARLIE=_Circrnas in Host And viRuses anaLysis pIpEline_. **8** SINCLAIR=_SINgle CelL AnalysIs Resource_. From 5bff48d9a6b902607c0a57c2a0626433ced50dd6 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 28 May 2026 16:55:56 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- profile/README.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/profile/README.md b/profile/README.md index 9291c23..5bd6712 100644 --- a/profile/README.md +++ b/profile/README.md @@ -132,19 +132,19 @@ CCBR offers end-to-end analysis pipelines for NGS data analysis. Here is a list of our prominent pipelines and their release schedule on BIOWULF: -| Data Type | Pipeline Name | Description | CLI\* available since | -| ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------- | ----------- | -------------------------------- | +| Data Type | Pipeline Name | Description | CLI\* available since | +| ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------- | | RNASeq1 | [RENEE](https://github.com/CCBR/RENEE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Comprehensive RNA-seq workflow that combines contamination screening, adapter trimming, two-pass STAR alignment, and RSEM quantification. It generates gene and isoform count matrices, fusion calls, and MultiQC-style quality summaries for cohort-level review. | July 3rd 2023 | -| WESSeq2 | [XAVIER](https://github.com/CCBR/XAVIER)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Whole-exome sequencing pipeline aligned to Broad-style best practices using a reproducible Snakemake execution model. It accepts FASTQ or BAM inputs and supports germline and somatic variant calling, CNV inference, and downstream annotation. | July 21st 2023 | -| ATACSeq3 | [ASPEN](https://github.com/CCBR/ASPEN)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | ATAC-seq analysis workflow for preliminary QC, peak calling, and differential chromatin accessibility testing. It is configured for Biowulf usage and provides standardized outputs for regulatory genomics interpretation. | November 30th 2023 | -| ChIPSeq4 | [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | ChIP-seq analysis pipeline with support for configurable reference genomes and optional spike-in genome handling. It produces reproducible peak-centric outputs from aligned sequencing data and can be run through CCBR module-based workflows. | October 15th 2023 | -| CRISPRSeq5 | [CRISPIN](https://github.com/CCBR/CRISPIN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | CRISPR screen sequencing workflow designed for reproducible run setup and execution on Biowulf. It processes screening libraries into analysis-ready outputs suitable for guide-level and gene-level interpretation. | September 2023 | -| CUT&RunSeq6 | [CARLISLE](https://github.com/CCBR/CARLISLE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | CUT&RUN pipeline that performs peak calling with MACS2, SEACR, and GoPeaks using spike-in-normalized FASTQ inputs. It is built in Snakemake and tuned for reproducible chromatin profiling on Biowulf. | October 31st 2023 | -| EV-Seq10 | [ESCAPE](https://github.com/CCBR/ESCAPE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Extracellular vesicle RNA-seq workflow for EV-derived libraries from raw reads through analysis-ready quantification outputs. It emphasizes consistent QC and standardized processing for comparative EV transcriptomics. | March 26th 2024 | -| circRNASeq7 | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | circRNA pipeline for detection, annotation, and quantification of host and viral circular RNAs. It orchestrates multiple circRNA callers in parallel, including CIRCExplorer2 and CIRI2-based paths, to support robust cross-method discovery. | September 16th 2024 | -| scRNASeq8 | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Single-cell analysis resource supporting multiple next-generation modalities in a reproducible Nextflow framework. It starts from FASTQ or h5-aligned inputs, performs per-sample QC, and generates per-contrast integration reports. | February 28th 2025 | -| WGSSeq9 | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Whole-genome sequencing pipeline based on Broad-aligned processing patterns and Nextflow orchestration. It calls and annotates germline and somatic variants, CNVs, and SVs with reproducible containerized execution. | May 31st 2025 | -| spatialSeq11 | [SPENCER](https://github.com/CCBR/SPENCER)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Spatial sequencing workflow for processing location-aware transcriptomic measurements across tissue regions. It is designed to produce structured outputs for downstream spatial feature analysis, integration, and visualization. | TBD | +| WESSeq2 | [XAVIER](https://github.com/CCBR/XAVIER)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Whole-exome sequencing pipeline aligned to Broad-style best practices using a reproducible Snakemake execution model. It accepts FASTQ or BAM inputs and supports germline and somatic variant calling, CNV inference, and downstream annotation. | July 21st 2023 | +| ATACSeq3 | [ASPEN](https://github.com/CCBR/ASPEN)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | ATAC-seq analysis workflow for preliminary QC, peak calling, and differential chromatin accessibility testing. It is configured for Biowulf usage and provides standardized outputs for regulatory genomics interpretation. | November 30th 2023 | +| ChIPSeq4 | [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | ChIP-seq analysis pipeline with support for configurable reference genomes and optional spike-in genome handling. It produces reproducible peak-centric outputs from aligned sequencing data and can be run through CCBR module-based workflows. | October 15th 2023 | +| CRISPRSeq5 | [CRISPIN](https://github.com/CCBR/CRISPIN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | CRISPR screen sequencing workflow designed for reproducible run setup and execution on Biowulf. It processes screening libraries into analysis-ready outputs suitable for guide-level and gene-level interpretation. | September 2023 | +| CUT&RunSeq6 | [CARLISLE](https://github.com/CCBR/CARLISLE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | CUT&RUN pipeline that performs peak calling with MACS2, SEACR, and GoPeaks using spike-in-normalized FASTQ inputs. It is built in Snakemake and tuned for reproducible chromatin profiling on Biowulf. | October 31st 2023 | +| EV-Seq10 | [ESCAPE](https://github.com/CCBR/ESCAPE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | Extracellular vesicle RNA-seq workflow for EV-derived libraries from raw reads through analysis-ready quantification outputs. It emphasizes consistent QC and standardized processing for comparative EV transcriptomics. | March 26th 2024 | +| circRNASeq7 | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | circRNA pipeline for detection, annotation, and quantification of host and viral circular RNAs. It orchestrates multiple circRNA callers in parallel, including CIRCExplorer2 and CIRI2-based paths, to support robust cross-method discovery. | September 16th 2024 | +| scRNASeq8 | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Single-cell analysis resource supporting multiple next-generation modalities in a reproducible Nextflow framework. It starts from FASTQ or h5-aligned inputs, performs per-sample QC, and generates per-contrast integration reports. | February 28th 2025 | +| WGSSeq9 | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Whole-genome sequencing pipeline based on Broad-aligned processing patterns and Nextflow orchestration. It calls and annotates germline and somatic variants, CNVs, and SVs with reproducible containerized execution. | May 31st 2025 | +| spatialSeq11 | [SPENCER](https://github.com/CCBR/SPENCER)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | Spatial sequencing workflow for processing location-aware transcriptomic measurements across tissue regions. It is designed to produce structured outputs for downstream spatial feature analysis, integration, and visualization. | TBD | \* CLI = Command Line Interface