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Adds Bowtie2 to address #476

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jfy133 merged 11 commits intodevfrom
bowtie2
Jun 23, 2020
Merged

Adds Bowtie2 to address #476
jfy133 merged 11 commits intodevfrom
bowtie2

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@jfy133 jfy133 commented Jun 23, 2020

nf-core/eager pull request

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@jfy133 jfy133 requested review from apeltzer and maxibor and removed request for apeltzer June 23, 2020 07:47
@jfy133 jfy133 changed the base branch from master to dev June 23, 2020 07:48
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@jfy133 jfy133 linked an issue Jun 23, 2020 that may be closed by this pull request
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Comment thread main.nf
trim5 = "${params.bt2_trim5}" != 0 ? "--trim5 ${params.bt2_trim5}" : ""
trim3 = "${params.bt2_trim3}" != 0 ? "--trim3 ${params.bt2_trim3}" : ""
bt2n = "${params.bt2n}" != 0 ? "-N ${params.bt2n}" : ""
bt2l = "${params.bt2l}" != 0 ? "-L ${params.bt2l}" : ""
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Update default

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@jfy133 jfy133 Jun 23, 2020

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I've addressed this in the docs and doesn't require update because it overrides the default from --bt2_sensitivity i.e. if you supply a value here it will override the default, otherwise the -N parameter is not supplied.

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A few modifications, mostly updating the default parameters

@jfy133 jfy133 mentioned this pull request Jun 23, 2020
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@jfy133 jfy133 requested review from apeltzer and maxibor June 23, 2020 09:46
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jfy133 and others added 2 commits June 23, 2020 11:50
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
@jfy133 jfy133 requested a review from apeltzer June 23, 2020 09:53
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Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
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jfy133 commented Jun 23, 2020

Anymore @maxibor ?(heh, rhyming)

@jfy133 jfy133 merged commit 1f32913 into dev Jun 23, 2020
@jfy133 jfy133 deleted the bowtie2 branch June 23, 2020 12:38
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Add BowTie2 support

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