{"push_id":1164499927,"size":9,"distinct_size":1,"ref":"refs/heads/sy-advance-reservation","head":"3e6ab5e716fb904d1fd0c74191f3e7659d3323c2","before":"531d5883509cede185cfcab749ff34ba7071e984","commits":[{"sha":"72573df89c061b5c7984f72e42a2b8005d30c4d1","author":{"name":"Hayden Metsky","email":"3793a0f8dee7086167cb3a3b08cea095f1759dc0@gmail.com"},"message":"Fix metagenomics input and provide more resources\n\nThe metagenomics tools took as input the file \"{sample}.bam\" in the\nsource subdir, but this file is not created when demultiplexing raw\ndata and the snakemake pipeline is not setup to create this file.\nThus, snakemake is unable to find input for the metagenomics tools.\nThis fix changes the input to be \"{sample}.raw.bam\" in the per_sample\nsubdir. The snakemake pipeline is able to create this file even\nwhen demultiplexing raw reads, so it is able to create input for\nthe metagenomics tasks.\n\nThis also gives the metagenomics tools more resources; it requests\nmore memory and a queue with longer runtime.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/72573df89c061b5c7984f72e42a2b8005d30c4d1"},{"sha":"380756d97e7e692500904f44a2baad62276bdec3","author":{"name":"Christopher Tomkins-Tinch","email":"8dfad6d927aac3c3ab8af37822ea93a5a40d7baa@broadinstitute.org"},"message":"add .raw.bam files to test_snake.py setup, to account for demultiplexing raw data","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/380756d97e7e692500904f44a2baad62276bdec3"},{"sha":"e458470eb63702af67eb6fcdfd2a5f0673ea9871","author":{"name":"Chris Tomkins-Tinch","email":"8dfad6d927aac3c3ab8af37822ea93a5a40d7baa@gmail.com"},"message":"Merge branch 'master' into hm-fix-metagenomics-input","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/e458470eb63702af67eb6fcdfd2a5f0673ea9871"},{"sha":"51fa323ac52d54da80d0bfa42a418615805f7804","author":{"name":"Chris Tomkins-Tinch","email":"8dfad6d927aac3c3ab8af37822ea93a5a40d7baa@gmail.com"},"message":"Merge branch 'master' into hm-fix-metagenomics-input","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/51fa323ac52d54da80d0bfa42a418615805f7804"},{"sha":"e59a64546d510dfdf2389df412f134e6169e04b1","author":{"name":"Chris Tomkins-Tinch","email":"8dfad6d927aac3c3ab8af37822ea93a5a40d7baa@gmail.com"},"message":"Merge branch 'master' into hm-fix-metagenomics-input","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/e59a64546d510dfdf2389df412f134e6169e04b1"},{"sha":"376be00ca4444c33678c29b54c52cbb545cce439","author":{"name":"Chris Tomkins-Tinch","email":"8dfad6d927aac3c3ab8af37822ea93a5a40d7baa@gmail.com"},"message":"Merge branch 'master' into hm-fix-metagenomics-input","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/376be00ca4444c33678c29b54c52cbb545cce439"},{"sha":"30ea705ee526b307642016d51d06aa70defcf4f7","author":{"name":"Simon Ye","email":"3b8e10480754ba93523db5dc4626a5f001e54bb7@yesimon.com"},"message":"Add link_transform func application in pipes\n\nIn SnakemakeRunner allow link name transformation and rename_raw_bam.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/30ea705ee526b307642016d51d06aa70defcf4f7"},{"sha":"18084302f98f706caa438ea8c11fd30b8b0ed4f9","author":{"name":"Daniel Park","email":"0ced81d16050e2b5451bbe792adea7fb490fffdd@broadinstitute.org"},"message":"Merge pull request #343 from broadinstitute/hm-fix-metagenomics-input\n\nFix metagenomics input and provide more resources","distinct":false,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/18084302f98f706caa438ea8c11fd30b8b0ed4f9"},{"sha":"3e6ab5e716fb904d1fd0c74191f3e7659d3323c2","author":{"name":"Daniel Park","email":"0ced81d16050e2b5451bbe792adea7fb490fffdd@broadinstitute.org"},"message":"Merge branch 'master' into sy-advance-reservation","distinct":true,"url":"https://api.github.com/repos/broadinstitute/viral-ngs/commits/3e6ab5e716fb904d1fd0c74191f3e7659d3323c2"}]}
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