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jpalmer37dfornika
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Make snippy report optional (#14)
* make snippy report optional * flipped logic to skip_report instead for backward compatibility * removed defaults channel from env * Bump version --------- Co-authored-by: Dan Fornika <dfornika@gmail.com>
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environments/environment.yml

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@@ -2,7 +2,6 @@ name: snippy-nf
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- python=3
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- csvkit=1.0.5

modules/snippy.nf

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@@ -44,14 +44,15 @@ process snippy {
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script:
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ram = task.memory ? ram = "--ram ${task.memory}" : ""
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report = params.skip_report ? "" : "--report"
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"""
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mkdir tmp
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snippy \
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--tmpdir ./tmp \
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--cpus ${task.cpus} \
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${ram} \
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--report \
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${report} \
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--prefix ${sample_id} \
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--mincov ${params.mincov} \
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--basequal ${params.basequal} \

nextflow.config

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@@ -1,7 +1,7 @@
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manifest {
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author = 'Dan Fornika'
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name = 'BCCDC-PHL/snippy-nf'
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version = '0.1.0'
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version = '0.1.1'
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description = 'BCCDC-PHL Nextflow wrapper for Snippy'
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mainScript = 'main.nf'
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nextflowVersion = '>=20.01.0'
@@ -19,6 +19,7 @@ params {
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mapqual = 60
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minfrac = 0
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outdir = 'results'
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skip_report = false
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pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
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pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
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}

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