CI
e0df82cfeb
Build pipeline: test-vsh-ci-build-template-zql9x
Source commit: 7fd732bb4e
Source message: v0.1.0
38 lines
1.0 KiB
Bash
Executable File
38 lines
1.0 KiB
Bash
Executable File
#/bin/bash
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OUT_DIR=resources_test/spatial_qc_sample_data
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[ ! -d "$OUT_DIR" ] && mkdir -p "$OUT_DIR"
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# fetch/create h5mu from somewhere
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cat > /tmp/qc.yaml <<EOF
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param_list:
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- id: xenium_tiny
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input: s3://openpipelines-bio/openpipeline_spatial/resources_test/xenium/xenium_tiny.h5mu
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- id: Lung5_Rep2_tiny
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input: s3://openpipelines-bio/openpipeline_spatial/resources_test/cosmx/Lung5_Rep2_tiny.h5mu
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var_name_mitochondrial_genes: mitochondrial
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var_name_ribosomal_genes: ribosomal
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output: '\$id.qc.h5mu'
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output_compression: gzip
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publish_dir: "$OUT_DIR"
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EOF
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nextflow run openpipelines-bio/openpipeline \
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-latest \
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-r 2.1.0 \
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-main-script target/nextflow/workflows/qc/qc/main.nf \
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-profile docker \
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-params-file /tmp/qc.yaml \
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-resume \
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-config src/configs/labels_ci.config
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# copy to s3
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aws s3 sync \
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--profile di \
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resources_test/spatial_qc_sample_data \
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s3://openpipelines-bio/openpipeline_incubator/resources_test/spatial_qc_sample_data \
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--delete --dryrun \
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--exclude "*" --include "*.h5mu" \
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