add workflow to download multiple SRA accessions to multiple bams: fetch_multiple_sra_to_bams #537
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…tch_multiple_sra_to_bams add workflow to download multiple SRA accessions to multiple bams: fetch_multiple_sra_to_bams; this is useful in the event a sample is associated with multiple sequencing runs (i.e. more than one SRR###). It also adjusts the Fetch_SRA_to_BAM task to find metadata for the requested run, in the event multi-run metadata is returned for a given accession
…) function not available until WDL >= 1.1)
name the output tsv file using the first specified ID since we are operating under WDL 1.0 (the `sep()` function is not available to join arrays of strings until WDL >= 1.1, and `~{sep="_" variable}` seemingly does not work outside a command block)
…dinstitute/viral-pipelines into ct-pluralize-fetch-sra-to-bam
dpark01
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May 4, 2024
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Thanks -- since I missed the use case motivating this I just have some questions:
- Would it be useful to emit a merged bam
Fileoutput at the workflow level (either instead of or in addition to theArray[File], again depending on the use case motivating this)? - I might feel better if we threw in a check / assertion that there is one and only one unique
biosample_accessionvalue across all the results. If that's not in conflict with the use case, maybe we can do that at the end of the workflow? - And if we can assume that, it might also be nice if the workflow could emit an output like
Map[String,String] biosample_metadata(which of course should be identical for all elements of the scatter so this just presents the deduplicated map). This would just contain the keys that start withsample_but not the other ones that are tied to the SRA entry.
try googleLegacyMachineSelection to set GCP machineType, per broadinstitute/cromwell@7fa57a0
ask for valid storage for N2 https://cloud.google.com/compute/docs/disks/local-ssd#choose_number_local_ssds
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add workflow to download multiple SRA accessions to multiple bams:
fetch_multiple_sra_to_bamsThis is useful in the event a sample is associated with multiple sequencing runs (i.e. more than one SRR###). It also adjusts the
Fetch_SRA_to_BAM taskto find metadata for the requested run in the event multi-run metadata is returned for a given accession.