Merge pull request #64 from CCBR/docs_readme

docs: Update readme

Author: dnousome

README.md

@@ -19,13 +19,15 @@ Original pipelining and code forked from the CCBR Exome-seek Pipeline [Exome-see
 [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 is installed on the Biowulf in the ccbrpipeliner module.
-Please clone this repository to your local filesystem using the following command:
+LOGAN can be used with the Nextflow pipelining software
+Please clone this repository to your local filesystem using the following command on Biowulf:
 ```bash
 # start an interactive node
 sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200
-# load the ccbrpipeliener module
-module load ccbrpipeliner
+git clone https://github.com/CCBR/LOGAN
+module load nextflow
+##Example run 
+nextflow run /data/LOGAN//main.nf
 ```
 
 ## Usage
@@ -89,17 +91,17 @@ c130889189_TUMOR  c130889189_PBMC
 
 #### 2.  Tumor only mode
 
-No flags are required
+No addtional flags for sample sheet are required as all samples will be used to call variants
 
 #### Calling Mode
 
 Adding flags determines SNV (germline and/or somatic), SV, and/or CNV calling modes
 
 `--vc`- Enables somatic SNV calling using mutect2, vardict, varscan, octopus, strelka (TN only), MUSE (TN only), and lofreq (TN only)
 
-`--germline`- Enables germline using DV
+`--germline`- Enables germline using Deepvariant
 
-`--sv`- Enables somatic SV calling using Manta and SVABA
+`--sv`- Enables somatic SV calling using Manta, SVABA, and GRIDSS (coming soon)
 
 `--cnv`- Enables somatic CNV calling using FREEC, Sequenza, and Purple (hg19/hg38 only)
 
@@ -111,33 +113,32 @@ Adding flags determines SNV (germline and/or somatic), SV, and/or CNV calling mo
 `--callers`- Comma separated argument for callers, the default is to use all available.  
 Example: `--callers mutect2,octopus`
 
-`--cnvcallers`- - Comma separated argument for cnvcallers. Adding flag allows only certain callers to run.  
+`--cnvcallers`- - Comma separated argument for CNV callers to use. Adding flag allows only certain callers to run.  
 Example: `--cnvcallers purple`
 
+`--svcallers`- - Comma separated argument for SV callers. Adding flag allows only certain callers to run.  
+Example: `--cnvcallers manta`
+
 
 ## Running LOGAN
 Example of Tumor_Normal 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 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -preview --vc --sv --cnv
+nextflow run /data/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 
-logan run --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -stub --vc --sv --cnv
+nextflow run /data/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
-logan run --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 /data/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 
 ```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" --callers octopus,mutect2 -preview --vc --sv --cnv
+nextflow run /data/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 
-logan run --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -stub --vc --sv --cnv
+nextflow run /data/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
-logan run --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 --vc --sv --cnv
+nextflow run /data/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
 ```