diff --git a/CHANGELOG.md b/CHANGELOG.md index f1ddc48..e880329 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,7 @@ # LOGAN development version - Now using the readthedocs theme for the docs website. (#84, @kelly-sovacool) +- LOGAN is now archived in Zenodo with DOI `10.5281/zenodo.14907169`. (#87, @kelly-sovacool) ## LOGAN 0.2.1 diff --git a/CITATION.cff b/CITATION.cff index 72984e8..804c73a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -21,3 +21,10 @@ title: "LOGAN: whoLe genOme-sequencinG Analysis pipeliNe" url: https://ccbr.github.io/LOGAN/ repository-code: https://github.com/CCBR/LOGAN license: MIT +type: software +identifiers: + - description: Archived snapshots of all versions + type: doi + value: 10.5281/zenodo.14907169 +version: v0.2.0 +date-released: "2025-02-21" diff --git a/README.md b/README.md index 6fd5159..e489fae 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,9 @@ -# LOGAN 🔬 +# LOGAN 🔬 **_whoLe genOme-sequencinG Analysis pipeliNe_** -[![build](https://github.com/abcsFrederick/LOGAN/actions/workflows/build.yml/badge.svg)](https://github.com/abcsFrederick/LOGAN/actions/workflows/build.yml) +[![build](https://github.com/CCBR/LOGAN/actions/workflows/build.yml/badge.svg)](https://github.com/CCBR/LOGAN/actions/workflows/build.yml) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14907169.svg)](https://doi.org/10.5281/zenodo.14907169) [![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) [![issues](https://img.shields.io/github/issues/ccbr/LOGAN?color=brightgreen)](https://github.com/ccbr/LOGAN/issues) [![license](https://img.shields.io/github/license/ccbr/LOGAN)](https://github.com/ccbr/LOGAN/blob/master/LICENSE) @@ -23,12 +24,14 @@ For more information about issues or trouble-shooting a problem, please checkout 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) ## Dependencies -**Requires:** `singularity>=3.5` `nextflow>=22.10.2` + +**Requires:** `singularity>=3.5` `nextflow>=22.10.2` [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. ## Setup -LOGAN can be used with the Nextflow pipelining software in + +LOGAN can be used with the Nextflow pipelining software in Please clone this repository to your local filesystem using the following command on Biowulf: ```bash @@ -37,72 +40,77 @@ sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200 git clone https://github.com/CCBR/LOGAN module load nextflow -##Example run +##Example run nextflow run LOGAN/main.nf -profile ci_stub -preview ``` ## Usage ### Input Files -LOGAN supports inputs of either -1) paired end fastq files + +LOGAN supports inputs of either + +1. paired end fastq files `--fastq_input`- A glob can be used to include all FASTQ files. Like `--fastq_input "*R{1,2}.fastq.gz"`. Globbing requires quotes. -2) Pre aligned BAM files with BAI indices +2. Pre aligned BAM files with BAI indices `--bam_input`- A glob can be used to include all FASTQ files. Like `--bam_input "*.bam"`. Globbing requires quotes. -3) A sheet that indicates the sample name and either FASTQs or BAM file locations +3. A sheet that indicates the sample name and either FASTQs or BAM file locations -`--fastq_file_input`- A headerless tab delimited sheet that has the sample name, R1, and R2 file locations +`--fastq_file_input`- A headerless tab delimited sheet that has the sample name, R1, and R2 file locations Example + ```bash c130863309_TUMOR /data/nousomedr/c130863309_TUMOR.R1_001.fastq.gz /data/nousomedr/c130863309_TUMOR.R2_001.fastq.gz c130889189_PBMC /data/nousomedr/c130889189_PBMC.R1_001.fastq.gz /data/nousomedr/c130889189_PBMC.R2_001.fastq.gz ``` - -`--bam_file_input` - A headerless tab delimited sheet that has the sample name, bam, and bam index (bai) file locations +`--bam_file_input` - A headerless tab delimited sheet that has the sample name, bam, and bam index (bai) file locations Example + ```bash c130863309_TUMOR /data/nousomedr/c130863309_TUMOR.bam /data/nousomedr/c130863309_TUMOR.bam.bai c130889189_PBMC /data/nousomedr/c130889189_PBMC.bam /data/nousomedr/c130889189_PBMC.bam.bai ``` ### Genome + `--genome` - A flag to indicate which genome to run. hg38, hg19 and mm10 are supported. Example: `--genome hg38` to run the hg38 genome -`--genome hg19` and `--genome mm10` are also supported +`--genome hg19` and `--genome mm10` are also supported + +#### hg38 has options for either -#### hg38 has options for either -`--genome hg38` - Based off the GRCh38.d1.vd1.fa which is consistent with TCGA/GDC processing pipelines +`--genome hg38` - Based off the GRCh38.d1.vd1.fa which is consistent with TCGA/GDC processing pipelines `--genome hg38_sf` - Based off the Homo_sapiens_assembly38.fasta which is derived from the Broad Institute/NCI Sequencing Facility The biggest difference between the two is that GRCh38.d1.vd1.fa only the GCA_000001405.15_GRCh38_no_alt_analysis_set, Sequence Decoys (GenBank Accession GCA_000786075), and Virus Sequences. Homo_sapiens_assembly38.fasta has HLA specific contigs which may not be compatible with certain downstream tools. - ### Operating Modes -#### 1. Paired Tumor/Normal Mode +#### 1. Paired Tumor/Normal Mode Required for Paired Tumor/Normal Mode -`--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. +`--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. Example + ```bash Tumor Normal c130863309_TUMOR c130863309_PBMC c130889189_TUMOR c130889189_PBMC ``` -#### 2. Tumor only mode +#### 2. Tumor only mode -No addtional flags for sample sheet are required as all samples will be used to call variants +No additional flags for sample sheet are required as all samples will be used to call variants #### Calling Mode @@ -116,8 +124,8 @@ Adding flags determines SNV (germline and/or somatic), SV, and/or CNV calling mo `--cnv` or `--copynumber`- Enables somatic CNV calling using FREEC, Sequenza, ASCAT, CNVKit, and Purple (hg19/hg38 only) - #### Optional Arguments + `--callers` - Comma separated argument for selecting only specified callers, the default is to use all. Example: `--callers mutect2,octopus` @@ -127,44 +135,46 @@ Example: `--cnvcallers purple` `--svcallers` - Comma separated argument for selecting only specified SV callers, the default is to use all. Example: `--svcallers gridss` -`--ffpe` - Adds additional filtering for FFPE by detecting strand orientation bias using SOBDetector. +`--ffpe` - Adds additional filtering for FFPE by detecting strand orientation bias using SOBDetector. `--exome` - When using exome data, this flag limits calling to intervals provided in target bed to reduce time and to account for exome sequencing specific parameters. An intervals file is required. `--indelrealign` - Enables indel realignment using the GATK pipeline when running alignment steps. May be helpful for certain callers (VarScan, VarDict) that do not have local haplotype reassembly. ## Running LOGAN -Example of Tumor_Normal calling mode + +Example of Tumor_Normal calling mode + ```bash -# preview the logan jobs that will run +# preview the logan jobs that will run nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -preview --vc --sv --cnv -# run a stub/dryrun of the logan jobs +# run a stub/dryrun of the logan jobs nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -stub --vc --sv --cnv # launch a logan run on slurm with the test dataset -nextflow run LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" --vc --sv --cnv +nextflow run LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" --vc --sv --cnv ``` -Example of Tumor only calling mode +Example of Tumor only calling mode + ```bash -# preview the logan jobs that will run +# preview the logan jobs that will run nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -preview --vc --sv --cnv -# run a stub/dryrun of the logan jobs +# run a stub/dryrun of the logan jobs nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -stub --vc --sv --cnv # launch a logan run on slurm with the test dataset nextflow run LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 --vc --sv --cnv ``` - ### Pipeline Tools and Overview -![alt text](docs/LOGAN.png) - +![alt text](docs/LOGAN.png) -## 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). +## 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 continuous 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). ## References + This repo was originally generated from the [CCBR Nextflow Template](https://github.com/CCBR/CCBR_NextflowTemplate). -**1.** Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459. +**1.** Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.