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Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

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Answers

  • arielyharielyh Member

    I'm new to firecloud. I have a bash script of bowtie2 alignment, samtools filtering and python post-processing of alignments, which successfully executed on my docker image. Now I would like to create a workspace to run it for many different samples or sample sets. I have two test sample bam files, which I already uploaded to google bucket. But I don't know how to import them into the metadata. I'm not fully understand the (howto) import metadata tutorial. After the metadata was created, I also like to run my analysis on FC. And there might be some error, because I'm learning how to write the WDL and set up the method configuration. If I come to today's (11/28/2018) office hour at Yosemite room, will there be someone to help me with this? Thanks in advance.

  • AdelaideRAdelaideR Member admin

    Hi @arielyh - Thank you for your question. We are working on it and we will get back to you.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @arielyh Yes, if you attend office hours there should be someone there to help you with your questions if you are having trouble following the documentation on how to import metadata!

  • arielyharielyh Member

    @SChaluvadi @Tiffany_at_Broad @AdelaideR Hi everyone, I figured out how to import the metadata from a file by myself. I used "the templates for uploading metadata into the data model", and also download some metadata from existing workspace to study. And then make my own file to upload.

    I still go to the office hour to ask help for writing the WDL and run the analysis. Although I was terribly late for the office hour, Khalid was still there. He helped me a lot on how to make the output directory and save my output in the WDL. He also taught me how to debug when my analysis has errors. And finally we got my analysis worked! I just want to thank Khalid again. Thanks for all his time and nice teaching. And thanks for everyone answering our questions here.

  • AdelaideRAdelaideR Member admin

    @arielyh Thank you for returning to add the solution to the forum. It is much appreciated! Thank you to Khalid for walking you through the WDL. Here is a document for other people who find this question and want to read about WDL:

    WDL Quick Start Guide

    WDL in Depth

    WDL Tutorials

  • WillyNWillyN Member

    Workflow run using workspace attribute didn't seem to work

    I have a workspace attribute, where the key is sample_to_fastq_list and value is "gs://fc-secure-17a69521-9cf8-4953-b394-c9e29de0e5d5/file_list.tsv" . It is of type string.

    In my method configuration, I set one of the inputs attribute to be workspace.sample_to_fastq_list. Running this workflow leads to a failure. It seems to not even run - it goes from submitted straight to failed. Furthermore, there is nothing in the logs indicating any kind of failure related to this.

    On a whim I decided to change the attribute to be the actual string "gs://fc-secure-17a69521-9cf8-4953-b394-c9e29de0e5d5/file_list.tsv" , and the workflow completed successfully. This seems to indicate an issue with the workspace attribute. Am I using the workspace attribute incorrectly?

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @WillyN Can you double check that when you are entering the Value corresponding to the Key sample_to_fastq_list, that there are no quotes around the Value? Here is a link that has a screenshot of what I am referring to. Please let us know if this works!

  • WillyNWillyN Member

    Thanks @SChaluvadi. Removing the quotes solves the problem. I do wish there was anything in the logs indicating some kind of problem there.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @WillyN I can pass your suggestion along to the team so that they can try to add better logging!

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