Feature/support external data #11
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KateSakharova
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Jul 1, 2024
KateSakharova
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- added samplesheet support for multiple runs
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| } | ||
| }, | ||
| "required": ["sample", "fastq_1"] | ||
| "required": ["study_accession","reads_accession", "fastq_1", "library_layout", "library_strategy"] |
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Just to confirm, these are all fields that will be received from prefect?
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To clarify, I see these will be overridden in the miassembler workflow when a samplesheet is used. So, are these still required fields?
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The idea is either to submit --study and --run-accession OR to use a samplesheet. The values from the samplesheet have the highest priority.
| "library_strategy": { | ||
| "type": "string", | ||
| "enum": ["metagenomic", "metatranscriptomic", "genomic", "transcriptomic", "other"], | ||
| "errorMessage": "library strategy should be only value from list: 'metagenomic', 'metatranscriptomic', 'genomic', 'transcriptomic', 'other'" |
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How will the "other" case be handled from prefect? e.g. in the case metadata are wrong and we realise the data are metaG/metaT and so on, is prefect going to default everything to "other" or is a manual input needed from us? In the latter case, what does "other" cover?
| "blast_reference_genomes_folder", | ||
| "bwamem2_reference_genomes_folder", | ||
| "outdir", | ||
| "human_phix_blast_index_name", |
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Would these two index names be required also in the other case?
