Fix STITCH to use chunks#11757
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SPPearce
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May 25, 2026
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| input: | ||
| tuple val(meta), path(collected_crams), path(collected_crais), path(cramlist), path(samplename), path(posfile), path(input, stageAs: "input"), path(genetic_map), path(rdata, stageAs: "RData_in"), val(chromosome_name), val(start), val(end), val(K), val(nGen) | ||
| tuple val(meta), path(collected_crams), path(collected_crais), path(cramlist), path(samplename), path(posfile), path(input, stageAs: "input"), path(genetic_map), path(rdata, stageAs: "RData_in"), val(chromosome_name), val(start), val(end), val(buffer), val(K), val(nGen) |
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Come, named inputs and save us from this abomination.
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The subworkflow was passing chunks to the module, but the module did not have any parameter to use regionStart and regionEnd, therefore, it was processing the whole chromosome. The changes here fix that.