added rawMetaDataset class #24
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marcmaxson
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Sep 24, 2019
* added batch_size parameter to run_pipeline * added CLI functionality * batch_size python/CLI and tests * removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists * Update setup.py * Update test_batch_size.py * Rename test_batch_size.py to test_pipeline_batch_size.py * dropped redundant tests and sped up one * Feature/public data (#21) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * version 1.1 (#22) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * progress bars * documenting `download` * Update cli.py * restore sample_name filter * added rawMetaDataset class and moved get_sample_sheet_s3 to more logical place here (#24) * updated docs for 1.1.1 * Update README.md * Update setup.py * exposed create_sample_sheet and download no_clean options * manifest file download in lambda * manifest file download in lambda * manifest file download in lambda * v1.1.3 bump bug fix * handles blank sample_name and ensures names are unique. * Update setup.py
marcmaxson
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Oct 8, 2019
* added batch_size parameter to run_pipeline * added CLI functionality * batch_size python/CLI and tests * removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists * Update setup.py * Update test_batch_size.py * Rename test_batch_size.py to test_pipeline_batch_size.py * dropped redundant tests and sped up one * Feature/public data (#21) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * version 1.1 (#22) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * progress bars * documenting `download` * Update cli.py * restore sample_name filter * added rawMetaDataset class and moved get_sample_sheet_s3 to more logical place here (#24) * updated docs for 1.1.1 * Update README.md * Update setup.py * exposed create_sample_sheet and download no_clean options * manifest file download in lambda * manifest file download in lambda * manifest file download in lambda * v1.1.3 bump bug fix * handles blank sample_name and ensures names are unique. * Update setup.py * geo downloader tweaks, fixed docs
marcmaxson
pushed a commit
that referenced
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Oct 18, 2019
* added batch_size parameter to run_pipeline * added CLI functionality * batch_size python/CLI and tests * removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists * Update setup.py * Update test_batch_size.py * Rename test_batch_size.py to test_pipeline_batch_size.py * dropped redundant tests and sped up one * Feature/public data (#21) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * version 1.1 (#22) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * progress bars * documenting `download` * Update cli.py * restore sample_name filter * added rawMetaDataset class and moved get_sample_sheet_s3 to more logical place here (#24) * updated docs for 1.1.1 * Update README.md * Update setup.py * exposed create_sample_sheet and download no_clean options * manifest file download in lambda * manifest file download in lambda * manifest file download in lambda * v1.1.3 bump bug fix * handles blank sample_name and ensures names are unique. * Update setup.py * geo downloader tweaks, fixed docs * minor tweaks to sample_sheet parser * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8
marcmaxson
pushed a commit
that referenced
this pull request
Oct 23, 2019
* added batch_size parameter to run_pipeline * added CLI functionality * batch_size python/CLI and tests * removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists * Update setup.py * Update test_batch_size.py * Rename test_batch_size.py to test_pipeline_batch_size.py * dropped redundant tests and sped up one * Feature/public data (#21) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * version 1.1 (#22) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * progress bars * documenting `download` * Update cli.py * restore sample_name filter * added rawMetaDataset class and moved get_sample_sheet_s3 to more logical place here (#24) * updated docs for 1.1.1 * Update README.md * Update setup.py * exposed create_sample_sheet and download no_clean options * manifest file download in lambda * manifest file download in lambda * manifest file download in lambda * v1.1.3 bump bug fix * handles blank sample_name and ensures names are unique. * Update setup.py * geo downloader tweaks, fixed docs * minor tweaks to sample_sheet parser * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8 * v1.1.9 minor bug fix to alt filename
marcmaxson
pushed a commit
that referenced
this pull request
Nov 5, 2019
* added batch_size parameter to run_pipeline * added CLI functionality * batch_size python/CLI and tests * removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists * Update setup.py * Update test_batch_size.py * Rename test_batch_size.py to test_pipeline_batch_size.py * dropped redundant tests and sped up one * Feature/public data (#21) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * version 1.1 (#22) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * progress bars * documenting `download` * Update cli.py * restore sample_name filter * added rawMetaDataset class and moved get_sample_sheet_s3 to more logical place here (#24) * updated docs for 1.1.1 * Update README.md * Update setup.py * exposed create_sample_sheet and download no_clean options * manifest file download in lambda * manifest file download in lambda * manifest file download in lambda * v1.1.3 bump bug fix * handles blank sample_name and ensures names are unique. * Update setup.py * geo downloader tweaks, fixed docs * minor tweaks to sample_sheet parser * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8 * v1.1.9 minor bug fix to alt filename * bug fix: sample QC control status * v1.1.11 generates meta_data pickle * Update config.yml * Update config.yml * Update config.yml * Update config.yml * coveralls
marcmaxson
pushed a commit
that referenced
this pull request
Nov 13, 2019
* added batch_size parameter to run_pipeline * added CLI functionality * batch_size python/CLI and tests * removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists * Update setup.py * Update test_batch_size.py * Rename test_batch_size.py to test_pipeline_batch_size.py * dropped redundant tests and sped up one * Feature/public data (#21) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * version 1.1 (#22) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * progress bars * documenting `download` * Update cli.py * restore sample_name filter * added rawMetaDataset class and moved get_sample_sheet_s3 to more logical place here (#24) * updated docs for 1.1.1 * Update README.md * Update setup.py * exposed create_sample_sheet and download no_clean options * manifest file download in lambda * manifest file download in lambda * manifest file download in lambda * v1.1.3 bump bug fix * handles blank sample_name and ensures names are unique. * Update setup.py * geo downloader tweaks, fixed docs * minor tweaks to sample_sheet parser * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8 * v1.1.9 minor bug fix to alt filename * bug fix: sample QC control status * v1.1.11 generates meta_data pickle * Update config.yml * Update config.yml * Update config.yml * Update config.yml * coveralls * bug fix * v1.1.14 smarter meta_data cli option * Create faq.md * Update faq.md * Update faq.md * Update faq.md * reworking download and meta_data to be more robust * Update faq.md * Update faq.md * downloader warns if idats aren't there; smarter meta_data * minor
marcmaxson
pushed a commit
that referenced
this pull request
Nov 14, 2019
* added batch_size parameter to run_pipeline * added CLI functionality * batch_size python/CLI and tests * removed test; changed default behavior: won't raise error if file-to-be-downloaded already exists * Update setup.py * Update test_batch_size.py * Rename test_batch_size.py to test_pipeline_batch_size.py * dropped redundant tests and sped up one * Feature/public data (#21) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * version 1.1 (#22) * download command, as well as some batch_size adjustments * fixed string issue * renaming update and removed redundant tests * bs4 required for Array ingester * tests * workaround to return objects with batch size changes * workaround to return objects with batch size changes * bug * tests pass for batch_size * progress bars * documenting `download` * Update cli.py * restore sample_name filter * added rawMetaDataset class and moved get_sample_sheet_s3 to more logical place here (#24) * updated docs for 1.1.1 * Update README.md * Update setup.py * exposed create_sample_sheet and download no_clean options * manifest file download in lambda * manifest file download in lambda * manifest file download in lambda * v1.1.3 bump bug fix * handles blank sample_name and ensures names are unique. * Update setup.py * geo downloader tweaks, fixed docs * minor tweaks to sample_sheet parser * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8: CLI retain --uncorrected mean prob values; sample_sheet sample_type sample_sub_type; sample_sheet accepts alt sentrix column headers * v1.1.8 * v1.1.9 minor bug fix to alt filename * bug fix: sample QC control status * v1.1.11 generates meta_data pickle * coveralls * bug fix * v1.1.14 smarter meta_data cli option * Create faq.md * reworking download and meta_data to be more robust * downloader warns if idats aren't there; smarter meta_data * minor * unit tests for download, meta_data, ae_download * v1.2.0 meta_data parser, better GEO/AE downloader
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and moved
get_sample_sheet_s3to more logical file location in this repo (from pipeline repo)