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CheckV - prophages fixes and post processing gff creation step #80

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merged 14 commits into from Jan 5, 2023
Merged

CheckV - prophages fixes and post processing gff creation step #80

merged 14 commits into from Jan 5, 2023

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mberacochea
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@mberacochea mberacochea commented Nov 25, 2022 •
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This PR includes:

  • A fix for prophages and chechV
  • GFF generation step

@mberacochea mberacochea marked this pull request as ready for review November 25, 2022 22:23
@mberacochea mberacochea self-assigned this Nov 25, 2022
@mberacochea
Revert changes that aren't needed.
b420578 
Revert basics container.
@mberacochea mberacochea mentioned this pull request Nov 26, 2022
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hoelzer
hoelzer reviewed Jan 2, 2023
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nextflow/configs/container.config
@@ -22,7 +22,7 @@ process {

withLabel: plot_contig_map {container = 'microbiomeinformatics/emg-viral-pipeline-plot-contig-map:v1' }
withLabel: virfinder { container = 'microbiomeinformatics/virfinder:v1.1__eb8032e' }
withLabel: checkV { container = 'microbiomeinformatics/checkv:v0.8.1' }
withLabel: checkV { container = 'microbiomeinformatics/checkv:v0.8.1__1' }
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just a recommendation: for such cases you could also, in general, add an md5 checksum to the container name. E.g. the first 5 characters of the md5 sum of the Dockerfile.

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Captured in #85

hoelzer
hoelzer reviewed Jan 2, 2023
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docker/checkv/Dockerfile
@@ -12,7 +12,7 @@ LABEL software.version="0.8.1"
ENV VERSION 0.8.1
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we could also bump all tool versions at some point. E.g. checkv is at 1.0.1 already. Not necessarily now, but maybe in another update

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Captured in #86

hoelzer
hoelzer approved these changes Jan 2, 2023
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Looks all good! I also did some test run! From my side +1 for merging. Will also check the PR #81 now

@mberacochea
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This also closes #77

@mberacochea mberacochea merged commit b420578 into dev Jan 5, 2023
@mberacochea mberacochea deleted the feature/post-processing-gff branch January 5, 2023 10:54
@mberacochea mberacochea restored the feature/post-processing-gff branch January 5, 2023 11:15
@mberacochea mberacochea deleted the feature/post-processing-gff branch January 5, 2023 11:23
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@hoelzer hoelzer hoelzer approved these changes

@Vkale1 Vkale1 Awaiting requested review from Vkale1

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@mberacochea @hoelzer @Vkale1