Commit 0a2bc8ad authored by Philippe BORDRON's avatar Philippe BORDRON
Browse files

Merge branch 'fix-alpha-rarefaction' into 'master'

Fix params that was ignored in alpha-rarefaction

See merge request !13
parents 7d8834fc 068115eb
Pipeline #31862 failed with stages
in 27 minutes and 49 seconds
......@@ -1154,10 +1154,11 @@ if "denoiser" in config["global"]:
getOutput("export_table_tsv", "alpha-rarefaction_maxdepth.txt")
output: getOutput("alpha_rarefaction", "alpha_rarefaction.qzv"),
getOutput("alpha_rarefaction", "results/index.html")
params: options = getOptions("alpha-rarefaction", ["p-max-depth"])
conda: qiime2_yml
shell: """
RAREFACTION_MAX_DEPTH=$(cat {input[3]})
qiime diversity alpha-rarefaction --i-table {input[0]} --i-phylogeny {input[1]} --m-metadata-file {input[2]} --o-visualization {output[0]} --p-max-depth $RAREFACTION_MAX_DEPTH
qiime diversity alpha-rarefaction --i-table {input[0]} --i-phylogeny {input[1]} --m-metadata-file {input[2]} --o-visualization {output[0]} --p-max-depth $RAREFACTION_MAX_DEPTH {params.options}
qiime tools export --input-path {output[0]} --output-path `dirname {output[1]}`
"""
......
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