 Sophia Chan | c0942d60b5e | raise exception so that people don't use this | | |
Sophia Chan | f0959031dcc | minor: added ncpus | | |
Sophia Chan | db6f53fcd4b | removed readme | | |
Sophia Chan | e2e2cc64193 | consistent arguments across pipelines | | |
Sophia Chan | 5cd9b9fc728M | Merge branch 'master' into dev_sc | | |
Sophia Chan | 2776983e5ee | consistent arguments across pipelines | | |
 Diljot Grewal | fca8b006adb | added version script | | |
Diljot Grewal | 4a04e2e09c2 | update:multiprocess bam to fastq, align, sort and reheader | | |
Diljot Grewal | bb43f24e95f | minor: added __init__ to realignment | | |
Diljot Grewal | ed40a4a9583 | improvement: one single job for the whole sample to avoid excessive downloading, refactoring | | |
 Andrew McPherson | e9ce96b323e | minor: updated create vm commands | | |
 Sophia Chan | 4d0009b0022 | minor: updated to use batch-mem by default | | |
Diljot Grewal | eb996b1f99f | minor: completed bwa mem mode, removed highmem pool, added multicore pool | | |
 Sophia Chan | a3dd6bd59ec | azure run files now consistent with other pipelines | | |
Sophia Chan | 689970e9979 | switch from low priority to dedicated nodes | | |
Andrew McPherson | d72074e64ef | cleaner script for running realignment | | |
 Ubuntu | cf6b4903384 | minor fixes | | |
Diljot Grewal | f5a46ae5495 | input: is now yaml, pep8 formatting, removed workflows/alignment | | |
Diljot Grewal | 6bd67cc0462 | inputfile: takes in sample id and output bam file path | | |
Diljot Grewal | 3936f9b6a4e | minor: moved components and alignment dir into realignment | | |
Sophia Chan | e627fc0c2c8 | new batch.yaml | | |
 Ubuntu | 8b7380446d3 | updated storage container name | | |
Ubuntu | 2bf50c13db7 | updated batch.yaml | | |
Ubuntu | 894305697c6 | remove ignored files | | |
Ubuntu | 7aa56c862fc | initial commit | | |
