Fix/sawfish_gcp_deloc#265
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williamrowell merged 2 commits intodevelop-v3from Nov 11, 2025
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- GCP delocalization script fails to delocalize sample-specific outputs using `read_lines()` (e.g. `Array[File] copynum_bedgraph`), but the task succeeds without errors, making this bug difficult to track - We don't want to use `glob()`, because it wouldn't necessarily maintain the sample order. - This patch generates the sample-specific output names as strings in advance and provides these to `sawfish_call` as an input. #263 broadinstitute/cromwell#5592
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* fix: Update stat_sv_DUP_count calculation to include `./1` calls. (#259) * fix: Sawfish output delocalization on GCP (#265) - GCP delocalization script fails to delocalize sample-specific outputs using `read_lines()` (e.g. `Array[File] copynum_bedgraph`), but the task succeeds without errors, making this bug difficult to track - We don't want to use `glob()`, because it wouldn't necessarily maintain the sample order. - This patch generates the sample-specific output names as strings in advance and provides these to `sawfish_call` as an input. - Closes #263 - Relates to broadinstitute/cromwell#5592 * bump: Update to Paraphase 3.4.0 (#266) * bump: Update Sawfish to v2.2.1 (#267) * bump: Update StarPhase to v2.0.0 (#268) * Update version numbers to v3.1.1
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read_lines()(e.g.Array[File] copynum_bedgraph), but the task succeeds without errors, making this bug difficult to trackglob(), because it wouldn't necessarily maintain the sample order.sawfish_callas an input.#263
broadinstitute/cromwell#5592