text: user3452: I have always used cellranger mkfastq to demultiplex 10x genomics runs manually, though recently the commands to do so have been incorporated into a script that should call the cellranger whenever it detects that a run is finished (and can be demultiplexed).
  The main difference when calling manually compared to being called automatically by the script is from where the commands are being called.
  So calling the commands manually from the directory where the samplesheet is and where the outputs shall be saved with:
  /home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=demux_10x --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc 
  
  does the job.
  but now cellranger is being called (automatically) from /home/ngs. The error message that I am getting from cellranger is:
  /home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/bin
  cellranger mkfastq (3.1.0)
  Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
  -------------------------------------------------------------------------------
  
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/tenkit/bin/_mkfastq: line 531: __/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/.mro: No such file or directory
  Martian Runtime - '3.1.0-v3.2.3'
  
  Invalid name: /nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ (only numbers, letters, dash, and underscore allowed)
  
  According to the error message I cannot use slashes / in the --id flag.
  Does anyone what I should pass to --id in order to get the outputs saved as
  /nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/?
  I already know that if I just pass --id=demux_10x the outputs will be saved at /home/ngs/demux_10x. (again, I am calling the script that calls cellranger from /home/ngs/)
  Obviously I could change to the desired output directory i.e. /nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/ and do --id=demux_10, though I am trying to avoid that for now.
  
  user3541: You should be able to use the --output-dir argument to specify a folder of your choice and use --id=demux_10x as before.
  
original_text: 3452: <p>I have always used <code>cellranger mkfastq</code> to demultiplex 10x genomics runs manually, though recently the commands to do so have been incorporated into a script that should call the <code>cellranger</code> whenever it detects that a run is finished (and can be demultiplexed).</p>
  
  <p>The main difference when calling manually compared to being called automatically by the script is <strong>from where</strong> the commands are being called.</p>
  
  <p>So calling the commands manually <strong>from the directory where the samplesheet is and where the outputs shall be saved</strong> with:</p>
  
  <pre><code>/home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=demux_10x --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc 
  </code></pre>
  
  <p>does the job.</p>
  
  <p>but now cellranger is being called (automatically) from <code>/home/ngs</code>. The error message that I am getting from cellranger is:</p>
  
  <pre><code>/home/ngs/installed/cellranger-3.1.0/cellranger mkfastq --id=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ --run=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX --samplesheet=/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/20200507_NovaSeq_129_Chromium_Anne_Fred_Samplesheet.csv --qc
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/bin
  cellranger mkfastq (3.1.0)
  Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
  -------------------------------------------------------------------------------
  
  /home/ngs/installed/cellranger-3.1.0/cellranger-cs/3.1.0/tenkit/bin/_mkfastq: line 531: __/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/.mro: No such file or directory
  Martian Runtime - '3.1.0-v3.2.3'
  
  Invalid name: /nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/ (only numbers, letters, dash, and underscore allowed)
  </code></pre>
  
  <p>According to the error message I cannot use slashes <code>/</code> in the <code>--id</code> flag.</p>
  
  <p>Does anyone what I should pass to <code>--id</code> in order to get the outputs saved as
  <code>/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/demux_10x/</code>?</p>
  
  <p>I already know that if I just pass <code>--id=demux_10x</code> the outputs will be saved at <code>/home/ngs/demux_10x</code>. (again, I am calling the script that calls <code>cellranger</code> from <code>/home/ngs/</code>)</p>
  
  <p>Obviously I could change to the desired output directory i.e. <code>/nexusb/Novaseq/200507_A00154_0492_AHL72WDRXX/</code> and do <code>--id=demux_10</code>, though I am trying to avoid that for now.</p>
   3541: <p>You should be able to use the <code>--output-dir</code> argument to specify a folder of your choice and use <code>--id=demux_10x</code> as before.</p>
  