Atac Seq PipEliNe :
CCBR recommends ASPEN to effectively analyze ATAC-seq datasets on the BIOWULF HPC system at the NIH.
module load ccbrpipeliner/7aspen --help##########################################################################################
Welcome to
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A_TAC_S_eq A_nalysis P_ip_E_li_N_e
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This pipeline was built by CCBR (https://bioinformatics.ccr.cancer.gov/ccbr)
Please contact Vishal Koparde for comments/questions (vishal.koparde@nih.gov)
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Here is a list of genome supported by aspen:
* hg19 [Human]
* hg38 [Human]
* mm10 [Mouse]
* mmul10 [Macaca mulatta(Rhesus monkey) or rheMac10]
* bosTau9 [Bos taurus(cattle)]
aspen calls peaks using the following tools:
* MACS2
* Genrich [RECOMMENDED FOR USE]
USAGE:
bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w/--workdir=<WORKDIR> -m/--runmode=<RUNMODE>
Required Arguments:
1. WORKDIR : [Type: String]: Absolute or relative path to the output folder with write permissions.
2. RUNMODE : [Type: String] Valid options:
* init : initialize workdir
* dryrun : dry run snakemake to generate DAG
* run : run with slurm
* runlocal : run without submitting to sbatch
ADVANCED RUNMODES (use with caution!!)
* unlock : unlock WORKDIR if locked by snakemake NEVER UNLOCK WORKDIR WHERE PIPELINE IS CURRENTLY RUNNING!
* reconfig : recreate config file in WORKDIR (debugging option) EDITS TO config.yaml WILL BE LOST!
* reset : DELETE workdir dir and re-init it (debugging option) EDITS TO ALL FILES IN WORKDIR WILL BE LOST!
* printbinds: print singularity binds (paths)
* local : same as runlocal
Optional Arguments:
--genome|-g : genome eg. hg38
--manifest|-s : absolute path to samples.tsv. This will be copied to output folder (--runmode=init only)
--help|-h : print this help
Example commands:
bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=init
bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=dryrun
bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=run
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VersionInfo:
python : python/3.10
snakemake : snakemake
pipeline_home : /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6
git commit/tag : f4366158ad972bc667422dcd4783bd69fa041556 v1.0.6
aspen_version : v1.0.6
##########################################################################################Visit ASPEN documentation for details.
For comments/suggestions/advice please reach out to Vishal Koparde or CCBR_Pipeliner. You can also open a new issue here.