Updating workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling from 0.4.2 to 0.4.3#37
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…artic-variant-calling from 0.4.2 to 0.4.3
| "amplicon_info": { | ||
| "id": 3, | ||
| "output_name": "output" | ||
| }, |
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Hmm, this changes WF behavior. ivar_removereads at the suggested wrapper version can compute amplicon info on the fly if the structure of its "input_bed" input allows. However, it also still accepts an amplicon_info dataset conditionally, and for backwards-compatibility that's the desired way to go (compare also the Changelog for galaxyproject#82).
So somehow potentially disrupting changes like this one (where an input_connection gets dropped) should be flagged by the bot. Not exactly sure how at the moment.
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It should be possible to flag the changes, I'll have a look at it.
I hope this can be considered as a nice future enhancement and not something that needs to be implemented straightaway though.
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I hope this can be considered as a nice future enhancement and not something that needs to be implemented straightaway though.
Absolutely, the suggestions are mostly really useful already!
Hello! This is an automated update of the following workflow: workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.
By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1should be updated totoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2should be updated totoolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2should be updated totoolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy0should be updated totoolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0should be updated totoolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy0should be updated totoolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy2toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1should be updated totoolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0The workflow release number has been updated from 0.4.2 to 0.4.3.