pipeSeq: repository for processing scripts of sequencing runs
npagane | risca lab
for detailed information/instructions: https://drive.google.com/open?id=1YnMXziT2NJixjEkBGW3VQeENGJyHzla7vpFuwQoDG-U

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available pipelines:
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fastq2bam (general processing)
ATACseq (runs fastq2bam + then calls peaks and other stats) 
CUTnTag (essentially just fastq2bam but with different alignment command)

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fastq2bam: align fastq data into bam format and produce quality metrics of the sequencing
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to run
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bash fastq2bam.sh -c <1> -f <2> -<opts>

where:
    <1> = desired working directory for processing (string, i.e. path/to/dir)
    <2> = directory with fastq files, presumably on store somewhere (string, i.e. path/to/fastq)
    -<opts> additional options:
        -g = genome reference for alignment (string, OPTS: 'hg38', 'hg19', 'mm9', 'mm10', etc.)
            default: hg38
        -b = blacklist for filtering (string, defaults to -g blacklist OR overwrite with path/to/blacklist)
            default: /rugpfs/fs0/risc_lab/store/risc_data/downloaded/hg38/blacklist/hg38-blacklist.v2.bed
        -m = the map quality threshold for alignment (int, i.e. 30)
            default: 30
        -p = any snakemake flags for compilation (string, i.e. --forcerun RULE)
            default: ""

* example *
bash fastq2bam.sh -c . -f /rugpfs/fs0/risc_lab/scratch/risc_data/FastqsFromBCLs 

all the other pipelines can be run as the same, just use "ATACseq.sh" or "CUTnTag.sh" rather than "fastq2bam.sh".
for specific optional arguments for each pipeline, run the executable (without any arguments) to see behavior.

* example help command *
bash ATACseq.sh

* example help output *
must specificy the desired working directory (-c) and fastq directory (-f).

USAGE: ATACseq.sh [-c .] [-f /rugpfs/fs0/risc_lab/store/risc_data/runs/FASTQs] [-s sample.txt]
  -c   PATH   path to where you want to process the sequencing data
  -f   PATH   path to where your FASTQ files live
OPTIONAL ARGUMENTS:
  -g=hg38      STRING  genome to align FATSQ files to (i.e. hg38, hg19, mm9, mm10, etc.)
  -b~hg38      PATH    path to where your blacklist file lives for filtering
  -m=30        INT     map quality threshold for alignment
  -p=''        STRING  additional snakemake flags and arguments for compilation
  --singleend          if FASTQ files are single-end rather than paired-end sequenced
  --help               print this usage text and exit

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environment
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must not be in any other conda environment except the pipeline you want to run (i.e. fastq2bam or ATACseq) 
or you can just be in the base env:
conda activate base

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file structure
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<pipeline>.sh <executable, such as fastq2bam or ATACseq or CUTnTag>
Snakefile <constructs pipeline through including rules>
rules/* <rules for pipeline along with any helper files>
scripts/* <R, python, or bash scripts to call in pipeline>
envs/* <stores indepedent and small conda environments for specific snakemake rules that would clash with main conda env>