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v1.3.6
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| Original file line number | Diff line number | Diff line change |
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| #!/bin/bash | ||
| set -e | ||
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| VER=$(cat chip.wdl | grep "#CAPER docker" | awk 'BEGIN{FS=":"} {print $2}') | ||
| DOCKER=encodedcc/chip-seq-pipeline:$VER | ||
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| # general | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/general -defaults example_input_json/dx/template_general.json | ||
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| # hg38 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/hg38 -defaults example_input_json/dx/template_hg38.json | ||
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| # hg19 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/hg19 -defaults example_input_json/dx/template_hg19.json | ||
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| # mm10 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/mm10 -defaults example_input_json/dx/template_mm10.json | ||
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| # mm9 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/mm9 -defaults example_input_json/dx/template_mm9.json | ||
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| # test sample PE ENCSR936XTK (full) | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/test_ENCSR936XTK -defaults example_input_json/dx/ENCSR936XTK_dx.json | ||
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| # test sample SE ENCSR000DYI (full) | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/test_ENCSR000DYI -defaults example_input_json/dx/ENCSR000DYI_dx.json | ||
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| # test sample SE ENCSR000DYI (subsampled, chr19/chrM only) | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/test_ENCSR000DYI_subsampled_chr19_only -defaults example_input_json/dx/ENCSR000DYI_subsampled_chr19_only_dx.json | ||
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| # test sample SE ENCSR000DYI (subsampled, chr19/chrM only, rep1) | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/test_ENCSR000DYI_subsampled_chr19_only_rep1 -defaults example_input_json/dx/ENCSR000DYI_subsampled_chr19_only_rep1_dx.json | ||
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| ## DX Azure | ||
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| # general | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/general -defaults example_input_json/dx_azure/template_general.json | ||
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| # hg38 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/hg38 -defaults example_input_json/dx_azure/template_hg38.json | ||
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| # hg19 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/hg19 -defaults example_input_json/dx_azure/template_hg19.json | ||
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| # mm10 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/mm10 -defaults example_input_json/dx_azure/template_mm10.json | ||
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| # mm9 | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/mm9 -defaults example_input_json/dx_azure/template_mm9.json | ||
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| # test sample PE ENCSR936XTK (full) | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/test_ENCSR936XTK -defaults example_input_json/dx_azure/ENCSR936XTK_dx_azure.json | ||
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| # test sample SE ENCSR000DYI (full) | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/test_ENCSR000DYI -defaults example_input_json/dx_azure/ENCSR000DYI_dx_azure.json | ||
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| # test sample SE ENCSR000DYI (subsampled, chr19/chrM only) | ||
| java -jar ~/dxWDL-0.79.1.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\"${DOCKER}\"}}") -f -folder /ChIP-seq2/workflows/$VER-dockerhub/test_ENCSR000DYI_subsampled_chr19_only -defaults example_input_json/dx_azure/ENCSR000DYI_subsampled_chr19_only_dx_azure.json |
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