Help with running the pipeline

[Chrisdoan9]

I tried to run the pipeline but as a new user, I got some difficulties. I have 8 fastq files and tried to make the files necessary to run the pipeline.

OS/Platform

• OS/Platform: SCG cluster

Input JSON file

Here is my json file:

{
    "atac.title" : “atac)”,
    "atac.description" : “Encode”,

    "atac.pipeline_type" : "atac",
    "atac.align_only" : false,
    "atac.true_rep_only" : false,

    "atac.genome_tsv" : "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv",

    "atac.paired_end" : true,

    "atac.fastqs_wt_rep1_R1" : [ "rep1_R1_L1.fastq.gz" ],
    "atac.fastqs_wt_rep1_R2" : [ "rep1_R2_L1.fastq.gz"],
    "atac.fastqs_wt_rep2_R1" : [ "rep2_R1_L1.fastq.gz" ],
    "atac.fastqs_wt_rep2_R2" : [ "rep2_R2_L1.fastq.gz" ],
    "atac.fastqs_di_rep1_R1" : [ "rep1_R1_L1.fastq.gz" ],
    "atac.fastqs_di_rep1_R2" : [ "rep1_R2_L1.fastq.gz"],
    "atac.fastqs_di_rep2_R1" : [ "rep2_R1_L1.fastq.gz" ],
    "atac.fastqs_di_rep2_R2" : [ "rep2_R2_L1.fastq.gz" ],

    "atac.auto_detect_adapter" : true,


    "atac.multimapping" : 4
}

I am not sure what to put in the input file because I see there is a section name input file in the instruction. Is it something like this?

    {

path/to/fastq.gz

    }

After having a correct json file, I should run:

caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name ANY_GOOD_LEADER_JOB_NAME

Is that correct? Thank you so much 😃.

[leepc12]

If you are working on SCG cluster, then run caper init slurm and follow instruction in the configuration file ~/.caper/default.conf (e.g. define slurm partition name).

Yes, replace "${INPUT_JSON}" with your input JSON file path. Your input JSON looks good.