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| # LOGAN 🔬 [](https://hub.docker.com/r/nciccbr/ccbr_wes_base) [](https://github.com/ccbr/LOGAN/issues) [](https://github.com/ccbr/LOGAN/blob/master/LICENSE) | ||
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| > **_LOGAN-whoLe genOme-sequencinG Analysis pipeliNe_**. This is the home of the LOGAN Pipeline. Its long-term goals: to accurately call germline and somatic variants, to infer CNVs, and to boldly annotate variants like no pipeline before! | ||
| > **_LOGAN-whoLe genOme-sequencinG Analysis pipeliNe_**. This is the home of the LOGAN Pipeline. Accurately call germline and somatic variants, CNVs, and SVs and annotate variants! | ||
| ## Overview | ||
| Welcome to LOGAN! Before getting started, we highly recommend reading through [LOGAN's documentation](https://ccbr.github.io/LOGAN). | ||
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| The **`./LOGAN`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions: | ||
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| * [<code>LOGAN <b>run</b></code>](https://ccbr.github.io/LOGAN/usage/run/): Run the WGS pipeline with your input files. | ||
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| LOGAN is a comprehensive whole genome-sequencing pipeline following the Broad's set of best practices. It relies on technologies like [Singularity<sup>1</sup>](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Nextflow<sup>2</sup>](https://nextflow.io/), a flexible and scalable workflow management system, to submit jobs to a cluster or cloud provider. | ||
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| The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FASTQ or BAM files and can be run locally on a compute instance, on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM. A hybrid approach ensures the pipeline is accessible to all users. | ||
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| Before getting started, we highly recommend reading through the [usage](https://ccbr.github.io/LOGAN/usage/run/) section of each available sub command. | ||
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| For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/ccbr/LOGAN/issues). | ||
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| Original pipelining and code forked heavily from the CCBR Exome-seek Pipeline [Exome-seek](https://github.com/mtandon09/CCBR_GATK4_Exome_Seq_Pipeline) | ||
| Original pipelining and code forked from the CCBR Exome-seek Pipeline [Exome-seek](https://github.com/CCBR/XAVIER) and [OpenOmics](https://github.com/openOmics/genome-seek) | ||
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| ## Dependencies | ||
| **Requires:** `singularity>=3.5` `nextflow>=22.10.2` | ||
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| [singularity](https://singularity.lbl.gov/all-releases) must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step relies on versioned images from [DockerHub](https://hub.docker.com/orgs/nciccbr/repositories). Nextflow uses singularity to pull these images onto the local filesystem prior to job execution, and as so, nextflow and singularity are the only two dependencies. | ||
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| ## Installation | ||
| ## Setup | ||
| LOGAN is installed on the Biowulf in the ccbrpipeliner module. | ||
| Please clone this repository to your local filesystem using the following command: | ||
| ```bash | ||
| # Clone Repository from Github | ||
| git clone https://github.com/ccbr/LOGAN.git | ||
| # Change your working directory | ||
| cd LOGAN/ | ||
| # start an interactive node | ||
| sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200 | ||
| # load the ccbrpipeliener module | ||
| module load ccbrpipeliner | ||
| ``` | ||
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| ## Usage | ||
| LOGAN supports either | ||
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| ### Input Files | ||
| LOGAN supports inputs of either | ||
| 1) paired end fastq files | ||
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| `--fastq_input`- A glob can be used to include all FASTQ files. Like `--fastq_input "*R{1,2}.fastq.gz"`. Globbing requires quotes | ||
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| 2) Pre aligned BAM files with BAI indices | ||
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| `--bam_input`- A glob can be used to include all FASTQ files. Like `--bam_input "*.bam"`. Globbing requires quotes | ||
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| 3) A sheet that indicates the sample name and either FASTQs or BAM file locations | ||
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| `--fastq_file_input`- A headerless tab delimited sheet that has the sample name, R1, and R2 file locations | ||
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| `--bam_file_input` - A headerless tab delimited sheet that has the sample name, bam and bai file locations | ||
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| ### Operating Modes | ||
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| #### 1. Paired Tumor/Normal Mode | ||
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| Required for Paired Tumor/Normal Mode | ||
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| `--sample_sheet` In Paired mode a sample sheet must be provided with the basename of the Tumor and Normal samples. This sheet must be Tab separated with a header for Tumor and Normal. | ||
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| #### 2. Tumor only mode | ||
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| No flags are required | ||
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| #### Calling Mode | ||
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| Adding flags determines SNV (germline and/or somatic), SV, and/or CNV calling modes | ||
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| `--vc`- Enables somatic SNV calling using mutect2, vardict, varscan, octopus, MUSE (TN only), and lofreq (TN only) | ||
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| `--germline`- Enables germline using DV | ||
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| `--sv`- Enables somatic SV calling using Manta and SVABA | ||
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| `--vc`- Enables somatic CNV calling using FREEC, Sequenza, and Purple (hg38 only) | ||
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| ## Running LOGAN | ||
| Example of Tumor only calling mode | ||
| ```bash | ||
| # copy the logan config files to your current directory | ||
| logan init | ||
| # preview the logan jobs that will run | ||
| logan run --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" -preview --vc --sv --cnv | ||
| # run a stub/dryrun of the logan jobs | ||
| logan run --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" -stub --vc --sv --cnv | ||
| # launch a logan run on slurm with the test dataset | ||
| logan run --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --vc --sv --cnv | ||
| ``` | ||
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| We currently support the hg38 and mm10 genomes. | ||
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| ## Contribute | ||
| This site is a living document, created for and by members like you. LOGAN is maintained by the members of CCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [repository](https://github.com/ccbr/LOGAN/pulls). | ||
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| ## References | ||
| This repo was originally generated from the [CCBR Nextflow Template](https://github.com/CCBR/CCBR_NextflowTemplate). | ||
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| <sup>**1.** Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.</sup> |