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Former User of DNAx Community_46

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Recent activity by Former User of DNAx Community_46

  • Range request to only download a BAM genomic interval

    Hi all, using WDL I would like to fetch a section (chrom:start-end) of a bam. I know I can do this using ```samtools view "the.bam" "chrom:start-end"``` nevertheless (am I wrong ?), before using th...

    • 1 follower
    • 1 comment
    • 0 votes

  • WDL: how to resume a failed workflow ? (caching)

    Hi all,   I'm now able to run a basic WDL workflow with the UK biobank data. I now wonder how avoid re-running the whole workflow is anything fails (equivalent of "-resume" in nextflow (https://ww...

    • 2 followers
    • 3 comments
    • 0 votes

  • WDL: File("dx;//file-id") vs dx download

    Hi again,   Looking at the WDL log, I saw that each time used a File input as `File("dx://file-id")` there was an hidden call to `dx download`. So am I right to say that each use of `File` in a...

    • 1 follower
    • 1 comment
    • 0 votes

  • WDL: what is the correct way to specify a docker/container ? ( The entity container-1234 could not be found )

    I'm trying to extract variants from a vcf file. My WDL task looks like this: ```task SEARCH_VARIANTS {   input {       File vcf       File bed       }   command <<<   set -e   set -x       bcftools...

    • 2 followers
    • 10 comments
    • 0 votes

  • WDL: how to specify a directory in the JSON input.

    My previous question (https://community.dnanexus.com/s/question/0D5t000004RYhxFCAT/wdl-specify-directory-as-input) was about the WDL syntax itself.  Now I want to specify a **directory** in the js...

    • 2 followers
    • 8 comments
    • 0 votes

  • WDL: specify directory as input.

    Hi(will I'm trying to run nextflow, I'm playing with small WDL workflows) I've got a workflow that needs a directory as input (I've got a task with `find ~ {dir} -type f (...)` ) It looks like Dire...

    • 2 followers
    • 4 comments
    • 0 votes

  • Import Nextflow: Exiting with nonzero exit code to report error

    Hi, after https://community.dnanexus.com/s/question/0D7t0000002P1zUCAS/ , I tried the NF importer. I started with https://gitlab.univ-nantes.fr/bioinfothorax/ukbbnf which is the clone of https://gi...

    • 2 followers
    • 2 comments
    • 0 votes

  • DNA nexus and nextflow

    Hi all,   this is my my first post here and as a newbie I'm afraid I'll have a bunch of questions.   So, here is my first one. I saw that there is a support for nextflow ( https://documentation.d...

    • 5 followers
    • 8 comments
    • 0 votes

  • dxfuse + bcftools " Input/output error" when reading.

    Hi,   I just tried dxfuse https://github.com/dnanexus/dxfuse I understand the dnanexus FS is NOT posix. I understand that the speed is limited by the banwidth . It worked fine to list the files...

    • 3 followers
    • 4 comments
    • 0 votes

  • WDL , docker and the "swiss army knife"

    If I'm not wrong, all the examples I saw so far with WDL require to pull the tools from docker. If my needs are only limited to the tools from the "swiss army knife" app, is there a way to run a ...

    • 3 followers
    • 4 comments
    • 0 votes