Answers.Body: <p>As explained in the <a href="https://pepkit.github.io/docs/sample_annotation/" rel="nofollow noreferrer">pep docs</a>, the <code>sample_name</code> column should be considered a unique identifier for a sample. The PEP requires that <strong>One row corresponds to one sample</strong> You have multiple rows with the same name; this is not allowed.</p>
  
  <p>You simply need to recast your annotation sheet such that it has <code>file1</code> and <code>file2</code> columns, but only 2 rows.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-18T01:16:24.287Z
Answers.LastActivityDate: 2018-01-18T08:00:34.270Z
Answers.LastEditDate: 2018-01-18T08:00:34.270Z
Answers.UserDisplayName: nsheff
Body: <p>I am using <a href="https://github.com/pepkit/looper" rel="nofollow noreferrer">Looper</a>. While running <code>looper run project_config.yaml</code> I am getting <code>duplicate sample name</code> error. I have two <code>fastq</code> files for each sample, so in the <code>annotation.csv</code> file I have:</p>
  
  <pre><code>sample_name,library,file
  abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r1.fq.gz
  abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r2.fq.gz
  abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r1.fq.gz
  abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r2.fq.gz
  </code></pre>
  
  <p>My <code>pipeline_interface.yaml</code> file looks the following way:</p>
  
  <pre><code>protocol_mapping:
    RNA-seq: sandro_rna_seq
  
  pipelines:
    sandro_rna_seq:
      name: sandro_rna_seq
      path: sandro_rna_seq.py  # relative to this 
  pipeline_interface.yaml file
      looper_args: True
      arguments:
        "-L": "IU"
        "-T": "gencode_mouse_m13"
        "-E": "/scratch/nv4e/binf-
  pipelines/bulk_rna_seq/salmon/pypiper/jyvo_experiment-metadata.yaml"
        "-C": "/scratch/nv4e/binf-
  pipelines/bulk_rna_seq/salmon/pypiper/salmon_rna_seq.yaml"
        "-X": "True"
        "-P": "6"
        "-I": sample_name
      resources:
        default:
          file_size: "0"
          cores: "20"
          mem: "120000"
  </code></pre>
  
  <p>Why am I getting this error? How could I fix it?</p>
  
Tags: <scrnaseq><looper><yaml>
Title: Looper: Duplicate sample name error
ThreadText: # Looper: Duplicate sample name error
  
  (Asked by: username_0 on 2018-01-18)
  
  I am using [Looper](https://github.com/pepkit/looper). While running `looper run project_config.yaml` I am getting `duplicate sample name` error. I have two `fastq` files for each sample, so in the `annotation.csv` file I have:
  
  ```
  sample_name,library,file
  abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r1.fq.gz
  abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r2.fq.gz
  abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r1.fq.gz
  abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r2.fq.gz
  
  ```
  
  My `pipeline_interface.yaml` file looks the following way:
  
  ```
  protocol_mapping:
    RNA-seq: sandro_rna_seq
  
  pipelines:
    sandro_rna_seq:
      name: sandro_rna_seq
      path: sandro_rna_seq.py  # relative to this 
  pipeline_interface.yaml file
      looper_args: True
      arguments:
        "-L": "IU"
        "-T": "gencode_mouse_m13"
        "-E": "/scratch/nv4e/binf-
  pipelines/bulk_rna_seq/salmon/pypiper/jyvo_experiment-metadata.yaml"
        "-C": "/scratch/nv4e/binf-
  pipelines/bulk_rna_seq/salmon/pypiper/salmon_rna_seq.yaml"
        "-X": "True"
        "-P": "6"
        "-I": sample_name
      resources:
        default:
          file_size: "0"
          cores: "20"
          mem: "120000"
  
  ```
  
  Why am I getting this error? How could I fix it?
  
  **Tags:** scrnaseq, looper, yaml
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-01-18. Score: 2 | Accepted answer
  
  As explained in the [pep docs](https://pepkit.github.io/docs/sample_annotation/), the `sample_name` column should be considered a unique identifier for a sample. The PEP requires that **One row corresponds to one sample** You have multiple rows with the same name; this is not allowed.
  
  You simply need to recast your annotation sheet such that it has `file1` and `file2` columns, but only 2 rows.
  
  
  ---
  
  