Rseq bamstat #155
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Rseq bamstat #155
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This reverts commit 38f586b.
KaiWaldrant
requested changes
Sep 27, 2024
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| engines: | ||
| - type: docker | ||
| image: ubuntu:22.04 |
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| image: ubuntu:22.04 | |
| image: python:3.10 |
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| - type: apt | ||
| packages: [ python3-pip ] |
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| - type: apt | |
| packages: [ python3-pip ] |
| argument_groups: | ||
| - name: "Input" | ||
| arguments: | ||
| - name: "--input" |
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Although the input parameter works I would use the parameter defined in the help page as the input parameter name.
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| - name: "--input" | |
| - name: "--input_file" |
| type: file | ||
| required: true | ||
| description: Input alignment file in BAM or SAM format. | ||
| - name: "--map_qual" |
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| - name: "--map_qual" | |
| - name: "--mapq" |
src/rseqc/rseqc_bamstat/script.sh
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| bam_stat.py \ | ||
| --input "${par_input}" \ | ||
| ${par_map_qual:+--mapq "${par_map_qual}"} \ |
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| ${par_map_qual:+--mapq "${par_map_qual}"} \ | |
| ${par_mapq:+--mapq "${par_mapq}"} \ |
src/rseqc/rseqc_bamstat/test.sh
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| echo "> Running $meta_functionality_name." | ||
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| "$meta_executable" \ | ||
| --input "$meta_resources_dir/test_data/$input_bam" \ |
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| --input "$meta_resources_dir/test_data/$input_bam" \ | |
| --input_file "$meta_resources_dir/test_data/$input_bam" \ |
src/rseqc/rseqc_bamstat/test.sh
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| "$meta_executable" \ | ||
| --input "$meta_resources_dir/test_data/$input_bam" \ | ||
| --output "$output_summary" \ | ||
| --map_qual 50 |
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| --map_qual 50 | |
| --mapq 50 |
src/rseqc/rseqc_bamstat/test.sh
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| echo "> Running $meta_functionality_name." | ||
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| "$meta_executable" \ | ||
| --input "$meta_resources_dir/test_data/$input_bam" \ |
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| --input "$meta_resources_dir/test_data/$input_bam" \ | |
| --input_file "$meta_resources_dir/test_data/$input_bam" \ |
src/rseqc/rseqc_bamstat/test.sh
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| echo ">>> Test 2: Test with non-default mapping quality threshold" | ||
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| output_summary="mapping_quality_mapq_30.txt" |
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| output_summary="mapping_quality_mapq_30.txt" | |
| output_summary="mapping_quality_mapq_50.txt" |
KaiWaldrant
reviewed
Sep 27, 2024
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Maybe we can subsample to half to get the file to about 10kb
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Thanks Kai, changes have been made! |
rcannood
approved these changes
Oct 26, 2024
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Description
Add RSeQC bamstat component
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributing guidelines
Proposed changes are described in the CHANGELOG.md
I have tested my code with
viash ns test --parallel -q <name or namespace>Check the correct box. Does this PR contain: