Body: <p>I am very new to ATAC-seq pipeline from Encode and trying to run on a HPC but not sure the steps after reading their instruction. <a href="https://github.com/ENCODE-DCC/atac-seq-pipeline" rel="nofollow noreferrer">https://github.com/ENCODE-DCC/atac-seq-pipeline</a>
  Here is my json file:</p>
  <pre><code>{
      &quot;atac.title&quot; : “atac)”,
      &quot;atac.description&quot; : “Encode”,
  
      &quot;atac.pipeline_type&quot; : &quot;atac&quot;,
      &quot;atac.align_only&quot; : false,
      &quot;atac.true_rep_only&quot; : false,
  
      &quot;atac.genome_tsv&quot; : &quot;https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv&quot;,
  
      &quot;atac.paired_end&quot; : true,
  
      &quot;atac.fastqs_wt_rep1_R1&quot; : [ &quot;rep1_R1_L1.fastq.gz&quot; ],
      &quot;atac.fastqs_wt_rep1_R2&quot; : [ &quot;rep1_R2_L1.fastq.gz&quot;],
      &quot;atac.fastqs_wt_rep2_R1&quot; : [ &quot;rep2_R1_L1.fastq.gz&quot; ],
      &quot;atac.fastqs_wt_rep2_R2&quot; : [ &quot;rep2_R2_L1.fastq.gz&quot; ],
      &quot;atac.fastqs_di_rep1_R1&quot; : [ &quot;rep1_R1_L1.fastq.gz&quot; ],
      &quot;atac.fastqs_di_rep1_R2&quot; : [ &quot;rep1_R2_L1.fastq.gz&quot;],
      &quot;atac.fastqs_di_rep2_R1&quot; : [ &quot;rep2_R1_L1.fastq.gz&quot; ],
      &quot;atac.fastqs_di_rep2_R2&quot; : [ &quot;rep2_R2_L1.fastq.gz&quot; ],
  
      &quot;atac.auto_detect_adapter&quot; : true,
  
  
      &quot;atac.multimapping&quot; : 4
  }
  </code></pre>
  <p>I also need input file so what it should be?</p>
  <blockquote>
  <p><strong>Input files</strong></p>
  <p>IMPORTANT: Our pipeline considers a replicate (rep) as a biological replicate. You can still define technical replicates for each bio replicate. Tech replicates will be merged together to make a single FASTQ for each bio replicate.</p>
  <p>IMPORTANT: Our pipeline supports up to 10 bio replicates.</p>
  <p>IMPORTANT: Our pipeline has cross-validation analyses (IDR/overlap) comparing every pair of all replicates. Number of tasks for such analyses will be like nC2. This number will be 45 for 10 bio replicates. It's recommended to keep number of replicates &lt;= 4.</p>
  <p>Pipeline can start from any of the following data types (FASTQ, BAM, NODUP_BAM and TAG-ALIGN).</p>
  <ol>
  <li>Starting from FASTQs</li>
  </ol>
  <ul>
  <li><p>Technical replicates for each bio-rep will be MERGED in the very early stage of the pipeline. Each read end R1 and R2 have separate arrays atac.fastqs_repX_R1 and atac.fastqs_repX_R2. Do not define R2 array for single-ended replicates.</p>
  </li>
  <li><p>Example of 3 paired-ended biological replicates and 2 technical replicates for each bio rep. Two technical replicates BIOREPX_TECHREP1.R1.fq.gz and BIOREPX_TECHREP2.R1.fq.gz for each bio replicate will be merged.</p>
  </li>
  </ul>
  <pre><code>       {
             &quot;atac.paired_end&quot; : true,
             &quot;atac.fastqs_rep1_R1&quot; : [&quot;BIOREP1_TECHREP1.R1.fq.gz&quot;, &quot;BIOREP1_TECHREP2.R1.fq.gz&quot;],
             &quot;atac.fastqs_rep1_R2&quot; : [&quot;BIOREP1_TECHREP1.R2.fq.gz&quot;, &quot;BIOREP1_TECHREP2.R2.fq.gz&quot;],
             &quot;atac.fastqs_rep2_R1&quot; : [&quot;BIOREP2_TECHREP1.R1.fq.gz&quot;, &quot;BIOREP2_TECHREP2.R1.fq.gz&quot;],
             &quot;atac.fastqs_rep2_R2&quot; : [&quot;BIOREP2_TECHREP1.R2.fq.gz&quot;, &quot;BIOREP2_TECHREP2.R2.fq.gz&quot;],
             &quot;atac.fastqs_rep3_R1&quot; : [&quot;BIOREP3_TECHREP1.R1.fq.gz&quot;, &quot;BIOREP3_TECHREP2.R1.fq.gz&quot;],
             &quot;atac.fastqs_rep3_R2&quot; : [&quot;BIOREP3_TECHREP1.R2.fq.gz&quot;, &quot;BIOREP3_TECHREP2.R2.fq.gz&quot;]
         }
  </code></pre>
  </blockquote>
  <p>How should I modify this command:</p>
  <pre><code>caper hpc submit atac.wdl -i &quot;${INPUT_JSON}&quot; --conda --leader-job-name ANY_GOOD_LEADER_JOB_NAME
  </code></pre>
  <p>I appreciate your help !</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-06T03:49:05.263Z
Comments.Text: This is very impressive - cross-validation cool. The thing I would check is this is can be run via **conda**, **docker** and **singularity** (you are using `--conda`). You need to know which one is recommended for your HPC.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-06T05:07:42.810Z
Comments.Text: Thank you . I usually run singularity.
Comments.UserDisplayName: Chris
Tags: <atac-seq><encode>
Title: Help with running ATAC-seq using Encode pipeline
ThreadText: # Help with running ATAC-seq using Encode pipeline
  
  (Asked by: username_0 on 2023-06-05)
  
  I am very new to ATAC-seq pipeline from Encode and trying to run on a HPC but not sure the steps after reading their instruction. <https://github.com/ENCODE-DCC/atac-seq-pipeline>
  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 also need input file so what it should be?
  
  > **Input files**
  >
  > IMPORTANT: Our pipeline considers a replicate (rep) as a biological replicate. You can still define technical replicates for each bio replicate. Tech replicates will be merged together to make a single FASTQ for each bio replicate.
  >
  > IMPORTANT: Our pipeline supports up to 10 bio replicates.
  >
  > IMPORTANT: Our pipeline has cross-validation analyses (IDR/overlap) comparing every pair of all replicates. Number of tasks for such analyses will be like nC2. This number will be 45 for 10 bio replicates. It's recommended to keep number of replicates <= 4.
  >
  > Pipeline can start from any of the following data types (FASTQ, BAM, NODUP\_BAM and TAG-ALIGN).
  >
  > 1. Starting from FASTQs
  >
  > * Technical replicates for each bio-rep will be MERGED in the very early stage of the pipeline. Each read end R1 and R2 have separate arrays atac.fastqs\_repX\_R1 and atac.fastqs\_repX\_R2. Do not define R2 array for single-ended replicates.
  > * Example of 3 paired-ended biological replicates and 2 technical replicates for each bio rep. Two technical replicates BIOREPX\_TECHREP1.R1.fq.gz and BIOREPX\_TECHREP2.R1.fq.gz for each bio replicate will be merged.
  >
  > ```
  >        {
  >            "atac.paired_end" : true,
  >            "atac.fastqs_rep1_R1" : ["BIOREP1_TECHREP1.R1.fq.gz", "BIOREP1_TECHREP2.R1.fq.gz"],
  >            "atac.fastqs_rep1_R2" : ["BIOREP1_TECHREP1.R2.fq.gz", "BIOREP1_TECHREP2.R2.fq.gz"],
  >            "atac.fastqs_rep2_R1" : ["BIOREP2_TECHREP1.R1.fq.gz", "BIOREP2_TECHREP2.R1.fq.gz"],
  >            "atac.fastqs_rep2_R2" : ["BIOREP2_TECHREP1.R2.fq.gz", "BIOREP2_TECHREP2.R2.fq.gz"],
  >            "atac.fastqs_rep3_R1" : ["BIOREP3_TECHREP1.R1.fq.gz", "BIOREP3_TECHREP2.R1.fq.gz"],
  >            "atac.fastqs_rep3_R2" : ["BIOREP3_TECHREP1.R2.fq.gz", "BIOREP3_TECHREP2.R2.fq.gz"]
  >        }
  >
  > ```
  
  How should I modify this command:
  
  ```
  caper hpc submit atac.wdl -i "${INPUT_JSON}" --conda --leader-job-name ANY_GOOD_LEADER_JOB_NAME
  
  ```
  
  I appreciate your help !
  
  **Tags:** atac-seq, encode
  
  > **Comments:**
  > **username_1**: This is very impressive - cross-validation cool. The thing I would check is this is can be run via **conda**, **docker** and **singularity** (you are using `--conda`). You need to know which one is recommended for your HPC.  
  > **username_0**: Thank you . I usually run singularity.  
  
  ---
  
  ## 0 answers
  
  