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Understanding workflow output | ||
============================= | ||
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@@ -8,4 +8,3 @@ Reference guides | |
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input | ||
params | ||
api |
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Input schema | ||
============ | ||
Input (samplesheet) schema | ||
========================== | ||
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The documentation below is automatically generated from the input schema and | ||
contains additional technical detail. | ||
The documentation below is automatically generated from the schema. The JSON | ||
file contains additional technical detail not shown in the table below. | ||
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.. jsonschema:: ../../assets/schema_input.json | ||
.. _`example`: https://github.com/PGScatalog/pgsc_calc/blob/master/assets/api_examples/input.json | ||
Each row in a samplesheet can only have a single genomic data format (i.e. they | ||
are mutually exclusive). | ||
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.. jsonschema:: ../../assets/schemas/target_genomes.json |
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docs/explanation/troubleshooting.rst → docs/troubleshooting.rst
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:orphan: | ||
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.. _troubleshoot: | ||
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Troubleshooting | ||
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process SCORE_REPORT { | ||
label 'process_high_memory' | ||
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conda (params.enable_conda ? "conda-forge::r-tidyverse=1.3.1 conda-forge::r-rsqlite=2.1.1" : null) | ||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
'oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/mulled-v2-e5054a4b868f4ffd21311d4e05426694e2c7fb5e:17fe01267c936fedcbd51470941b075c42b08c23-0' : | ||
'dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/mulled-v2-e5054a4b868f4ffd21311d4e05426694e2c7fb5e:17fe01267c936fedcbd51470941b075c42b08c23-0' }" | ||
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input: | ||
path scorefiles | ||
path report | ||
path logo | ||
path db | ||
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output: | ||
path "*.html" , emit: report | ||
path "*.txt" , emit: scores | ||
path "versions.yml", emit: versions | ||
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script: | ||
def args = task.ext.args ?: '' | ||
""" | ||
# dumb workaround symlink & out_dir (rmarkdown) | ||
cp $report report.rmd | ||
R -e 'rmarkdown::render("report.rmd", \ | ||
output_options = list(self_contained=TRUE))' | ||
cat <<-END_VERSIONS > versions.yml | ||
${task.process.tokenize(':').last()}: | ||
R: \$(echo \$(R --version 2>&1) | head -n 1 | cut -f 3 -d ' ') | ||
END_VERSIONS | ||
""" | ||
} |
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