update Dockerfile and Makefile for Canu version update. add parameter in Canu.wdl. #376
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SHuang-Broad
requested changes
Mar 29, 2023
| TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest | ||
| VERSION = 0.2.0 | ||
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| TAG1 = us.gcr.io/broad-dsp-lrma/lr-canu:$(VERSION) |
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Need to revert back to the old way.
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| build_no_cache: | ||
| docker build --no-cache -t $(TAG1) -t $(TAG2) . | ||
| docker build -t $(TAG1) -t $(TAG2) . |
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check tabs and spaces
| Int disk_size = 150 * ceil(size(reads, "GB")) | ||
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| command <<< | ||
| set -euxo pipefail | ||
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| canu -correct \ | ||
| canu -correct corOutCoverage=~{corrected_coverage}\ |
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add space at then end of the line
| -p ~{prefix} -d canu_correct_output \ | ||
| genomeSize=~{genome_size}m \ | ||
| genomeSize=~{genome_size}k \ |
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rename the variable to genome_sz_in_kb
| Int disk_size = 50 * ceil(size(corrected_reads, "GB")) | ||
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| command <<< | ||
| set -euxo pipefail | ||
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| canu -trim \ | ||
| -p ~{prefix} -d canu_trim_output \ | ||
| genomeSize=~{genome_size}m \ | ||
| genomeSize=~{genome_size}k \ |
| Int disk_size = 50 * ceil(size(trimmed_reads, "GB")) | ||
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| command <<< | ||
| set -euxo pipefail | ||
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| canu -assemble \ | ||
| -p ~{prefix} -d canu_assemble_output \ | ||
| genomeSize=~{genome_size}m \ | ||
| genomeSize=~{genome_size}k \ |
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updated Dockerfile and Makefile for Canu2.2 version update.
added "technology" parameter in Canu.wdl to specify nanopore vs pacbio sequencing method