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Add merqury to pipeline #42

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chriswyatt1 opened this issue Oct 23, 2024 · 3 comments · Fixed by #63
Closed

Add merqury to pipeline #42

chriswyatt1 opened this issue Oct 23, 2024 · 3 comments · Fixed by #63
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@stephenturner
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enhancement New feature or request

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@chriswyatt1
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Example from Usman: https://github.com/Plant-Food-Research-Open/assemblyqc

Used in genome only mode. Already an nf-core module
@chriswyatt1 chriswyatt1 added the enhancement New feature or request label Oct 25, 2024
@stephenturner stephenturner self-assigned this Oct 28, 2024
@stephenturner stephenturner moved this from Todo to In Progress in Hackathon October 2024 Oct 28, 2024
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Also needs meryl for building kmer dbs for merqury

@stephenturner stephenturner mentioned this issue Oct 28, 2024
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stephenturner added a commit to stephenturner/genomeqc that referenced this issue Oct 28, 2024
@stephenturner
add merqury and meryl modules to json with nf-core tools genomeqc/nf-…
8a0a2df 
…core#42 genomeqc/nf-core#58
@stephenturner stephenturner mentioned this issue Oct 28, 2024
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@chriswyatt1
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Could you add a PR?. May be easier to think about how to integrate it

@stephenturner stephenturner mentioned this issue Oct 28, 2024
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Draft PR in #63 with more info

@stephenturner stephenturner mentioned this issue Oct 29, 2024
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stephenturner added a commit to stephenturner/genomeqc that referenced this issue Oct 29, 2024
@stephenturner
merqury_skip = false in test profile nf-core#62 nf-core#42
bd55499
stephenturner added a commit to stephenturner/genomeqc that referenced this issue Oct 29, 2024
@stephenturner
run merqury if providing fastq file nf-core#62 nf-core#42
9615c08
@stephenturner stephenturner mentioned this issue Oct 29, 2024
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@github-project-automation github-project-automation bot moved this from In Progress to Done in Hackathon October 2024 Oct 29, 2024
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@stephenturner stephenturner

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enhancement New feature or request
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Hackathon October 2024
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Add meryl and merqury stephenturner/genomeqc
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@stephenturner @chriswyatt1