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...

• Former User of DNAx Community_46
• 06 October 2023 00:00
• 1 follower
• 1 comment
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The following code worked: ```   runtime {               cpu : 1               memory : "1GB"      docker: "quay.io/biocontainers/bcftools:1.16--hfe4b78e_1"       }``` (Thanks to the B Slavik / UK...

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• 22 February 2023 08:22
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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...

• Former User of DNAx Community_46
• 22 February 2023 00:00
• 2 followers
• 3 comments
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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...

• Former User of DNAx Community_46
• 22 February 2023 00:00
• 1 follower
• 1 comment
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changing the json object to a plain string produces the following error ( dx version is dx v0.338.1 ) ```dxpy.exceptions.InvalidInput: i/o value bed needs to be given using DNAnexus links, code 422...

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• 16 February 2023 14:17
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OK, here is a working solution Using the WDL keyword `directory ` was a bad choice. A better solution was to use a String containing the path to the directory and to call `dx find data` to get a ...

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• 16 February 2023 10:24
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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...

• Former User of DNAx Community_46
• 16 February 2023 00:00
• 2 followers
• 10 comments
• 0 votes

Thanks, I'll try this tomorrow. But then, in `Array[String] files |` I'll get a list of file-id , say the IDs of VCF files. How will I give those ID to bcftools ?  ```bcftools view 'dx:PROJ...

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• 15 February 2023 16:22
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yes the code is compiled and launched. But it fails when the directory is used. For now I tried to put a string as the value of "dir_name" in the JSON file.I'll try without json tomorrow.  For now,...

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• 15 February 2023 16:03
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