<div dir="auto">Hi Sehrish,<div dir="auto"><br></div><div dir="auto">Can you provide the whole output, and the command line you used?</div><div dir="auto"><br></div><div dir="auto">Thanks,</div><div dir="auto">Peter</div><div dir="auto"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Jun 25, 2017 11:15, "Sehrish Kanwal" <<a href="mailto:skanwal@student.unimelb.edu.au">skanwal@student.unimelb.edu.au</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="m_2464111617755397987gmail-linestyle1 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px">Hi, </div><div class="m_2464111617755397987gmail-linestyle1 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px"><br></div><div class="m_2464111617755397987gmail-linestyle1 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px">I am new to arvados and trying to run my cwl workflow using it. I have setup my VM and have the directory structure setup like the one I had at my local machine.</div><div class="m_2464111617755397987gmail-linestyle2 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px">I am getting an error: Field `run` contains undefined reference to `file:///data-sdc/home/skanw al/keep2/home/New%<wbr>20collection/BWA-mem.cwl`</div><div class="m_2464111617755397987gmail-linestyle1 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px">I think that is something to do with referencing files using/in keep. Can someone help me with that? More specifically how can I run my cwl workflow on arvados? What requirements do I need to fulfil before trying that?</div><div class="m_2464111617755397987gmail-linestyle1 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px">Thanks.</div><div class="m_2464111617755397987gmail-linestyle1 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px"><br></div><div class="m_2464111617755397987gmail-linestyle1 m_2464111617755397987gmail-colourline" style="font-family:consolas,'lucida console',monospace;padding-left:7px;word-wrap:break-word;color:rgb(0,0,0);font-size:12.8px"><br></div><div><div class="m_2464111617755397987gmail_signature"><div dir="ltr"><div><span style="font-family:verdana,sans-serif">Kind Regards,</span></div><div><span style="font-family:verdana,sans-serif">Sehrish Kanwal<br></span></div><span style="font-family:verdana,sans-serif">
</span><div><span style="font-family:verdana,sans-serif">PhD Research Scholar<br></span></div><div><span style="font-family:verdana,sans-serif">Computing and Information Systems, Melbourne School of Engineering<br></span></div><div><span style="font-family:verdana,sans-serif">The University of Melbourne</span></div>
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