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Hello :)
I have a question regarding viral-ngs and its capabilities for detecting virus integration and outputting the results to a text file. I tried to understand the explanation provided in the …
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Currently I have to set world-writable for host user data directory so that docker can write to this via `data` volume. So I propose the following solution so that docker can have the same read/write …
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I've used kneaddata for some time. It is quite robust with its features. I felt it is more flexible to use than current viral-ngs handlings of quality controls. So maybe `viral-ngs` can borrow `knead…
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Hi, @rasmushenningsson
I am wondering to know can DISSEQT be used with virus multiple sequences alignment (MSA) collected from different dates?
If I was understood correctly, DISSEQT used NGS data…
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The [viral-ngs-fasta-fetcher](https://github.com/dnanexus/viral-ngs/blob/dnanexus/viral-ngs-fasta-fetcher/src/viral-ngs-fasta-fetcher.sh) currently requires the user to input his or her email address.…
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Add `dustmasker` as a tool to viral-ngs for pre-processing of metagenomics databases (removal of low-complexity sequences). It's part of the blast toolset so the `Tool` subclass should perhaps be adde…
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[Cromwell version 32](https://github.com/broadinstitute/cromwell/releases/tag/32) starts the transition from PAPIv1 to PAPIv2 and signals the future deprecation some of the old "JES" terminology (the …
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In a few places we use `.sam` intermediary files where we could use `.bam` files. The latter take a bit more IO/CPU time with the advantage of better compression ratio. One such instance is here:
htt…
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Hi, I added a recipe for cromwell to the bioconda channel:
https://github.com/bioconda/bioconda-recipes/tree/master/recipes/cromwell
Updating it is currently a manual affair, mostly consisting of …
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When the 'docker' runtime attribute of a task is specified with the sha256 hash, as in
runtime {
docker: "quay.io/broadinstitute/viral-ngs:1.22.0@sha256:be458fe91e176102c9c8e2933c9ff430d…