fix: RSEM-calculate-expression wrapper with FASTQ-files as input + Integration of test case #970
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added 2 commits
January 5, 2023 17:45
KuechlerO
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johanneskoester
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Jan 20, 2023
johanneskoester
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Jan 20, 2023
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| - reference: One of the index files created by rsem-prepare-reference; the file suffix is stripped and passed on to rsem | ||
| - reference_bowtie: Only needed for FASTQ input; One of the bowtie index files created by bowtie-build |
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We should rather require all index files. multiext can be used for that. Otherwise, the wrapper only works on shared filesystems.
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Ok, I've now employed multiext as requested.
johanneskoester
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🤖 I have created a release \*beep\* \*boop\* --- ### [1.21.4](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.21.3...v1.21.4) (2023-01-20) ### Bug Fixes * channel definitions for cooltools (and update version to 0.5.2), genefuse, genomescope, qualimap and meryl ([#980](https://www.github.com/snakemake/snakemake-wrappers/issues/980)) ([26271ac](https://www.github.com/snakemake/snakemake-wrappers/commit/26271acfb27c02d51d2a8cc0922b4780998e6b53)) * RSEM-calculate-expression wrapper with FASTQ-files as input + Integration of test case ([#970](https://www.github.com/snakemake/snakemake-wrappers/issues/970)) ([ea9c897](https://www.github.com/snakemake/snakemake-wrappers/commit/ea9c8978259c87156f4e48711eed0172a8966209)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Description
--bam->--alignments)input_bam = FalseNotes
The original provided test-case from the authors for BAM-file inputs includes only an empty BAM-file (except of the header). My test case also includes reads, which do not map to the reference sequence (since the provided reference sequence is too short anyways). So as I understand, the purpose of these tests is just to ensure, whether the pipeline is able to run through. However, to make it more robust additional tests with real working examples would be needed.