Jennifer Shelton 28769507040 M Pull request #8: fix: reprep tools Merge in WDL/somatic_dna_tools from annotation to master
* commit '45057760ebe767c45a70cfb9529982c3e4e88b90':
fix: add prefix when renaming metadata 02 Oct 2023 Jennifer Shelton 45057760ebe fix: add prefix when renaming metadata 29 Sep 2023 Jennifer Shelton a4007334b2d feat: handle external annotations 21 Aug 2023 Jennifer Shelton 8ea218a20b7 feat: remove unneeded mnv vcf 16 Jul 2023 Jennifer Shelton cfd52e7e7d8 fix: whitespace 16 Jul 2023 Jennifer Shelton 9827cd69ed7 M pull online changes Merge branch 'annotation' of https://bitbucket.nygenome.org/scm/wdl/somatic_dna_tools into annotation 16 Jul 2023 Jennifer Shelton 5036b0c24d8 feat: split mnv calls out into mnv vcf 16 Jul 2023 Jennifer Shelton 92a670473c2 feat: split into the max number of files (evenly) if spliting by every n variant calls makes too many files 14 Jul 2023 Jennifer Shelton 1fdcbb97799 feat: filter updated non-cancer germline vars from Gnomad/1000G 11 Jul 2023 Jennifer Shelton f409e79c952 draft: changes to germ fileter 11 Jul 2023 Jennifer Shelton 9cf13be5b90 feat: files for refactored pipeline 08 Jul 2023 Jennifer Shelton 237d6f1e88b feat: add max number of files to create 23 Jun 2023 Jennifer Shelton 8440786f30e M Pull request #5: Mutect2 rate threshold Merge in WDL/somatic_dna_tools from mutect2_rate_threshold to master
* commit '84c0fe4989e3b2cbbea0eda6d10fe3516162507b':
fix: lookup deleted nucleotides
fix: lookup deleted nucleotides
feat: gracefully handle timeouts
feat: gracefully handles errors reading bams from buckets
fix: break more of script into sections
feat: handle input without any markers
feat: runs on gcs bams
f... 17 May 2023 Jennifer Shelton 84c0fe4989e fix: lookup deleted nucleotides 16 May 2023 Jennifer Shelton 5d990aecd90 fix: lookup deleted nucleotides 16 May 2023 Jennifer Shelton aec294ce54a M pull online changes Merge branch 'mutect2_rate_threshold' of https://bitbucket.nygenome.org/scm/wdl/somatic_dna_tools into mutect2_rate_threshold 16 May 2023 Jennifer Shelton fffdec255ef feat: gracefully handle timeouts 16 May 2023 Jennifer Shelton 5b8a77bedef feat: gracefully handles errors reading bams from buckets 16 May 2023 Jennifer Shelton fad8f5ec3d9 fix: break more of script into sections 15 May 2023 Jennifer Shelton d59dbbbdd5d feat: handle input without any markers 15 May 2023 Jennifer Shelton 37ac756c17e feat: runs on gcs bams 12 May 2023 Jennifer Shelton 415483a70d3 feat: add file for calling merge 09 May 2023 Jennifer Shelton e1cc239ced6 feat: add file for calling merge 09 May 2023 Jennifer Shelton 0931cf872b4 feat: add file for callin merge 09 May 2023 Jennifer Shelton 5e4ce9fbe01 feat: compare two strings and return an empty file for mismatch and a file with content if they match (to avoid read_ errors on HPC clusters) 08 May 2023 Jennifer Shelton 8cb74b3a399 M Pull request #4: Mutect2 rate threshold Merge in WDL/somatic_dna_tools from mutect2_rate_threshold to master
* commit '190f30c6d131b3b632edda4330ce727cadd9b2b7':
feat: feed in sample ids in case where order must be swapped
feat: add mutect2 rate tool
feat: write to file drop na lines
tests: add in tests for tools
feat: split VCF files
feat: get pileup without localization handle multi id entires
tests: add in tests for... 03 May 2023 Jennifer Shelton 190f30c6d13 feat: feed in sample ids in case where order must be swapped 28 Apr 2023 Jennifer Shelton ab6eb574bff feat: add mutect2 rate tool 28 Apr 2023 Jennifer Shelton 095fd8f4421 feat: write to file drop na lines 28 Apr 2023 Jennifer Shelton e0ce3a8d544 tests: add in tests for tools 23 Apr 2023 Jennifer Shelton 055cc7076a3 feat: split VCF files 23 Apr 2023 Jennifer Shelton a9c02493de8 feat: get pileup without localization handle multi id entires 23 Apr 2023 Jennifer Shelton 2189098c537 tests: add in tests for tools 21 Apr 2023 Jennifer Shelton e088a8a4407 feat: minor changes based on pytest results 21 Apr 2023 Jennifer Shelton c1f50a046bb M Pull request #3: feat: allow for input cram files that don't need to be updated Merge in WDL/somatic_dna_tools from jshelton/update_cram_infopy-1680191320951 to master
* commit '6747583da8c46da97d99de807b815d48475756d2':
style: standardize whitespace
feat: allow for input cram files that don't need to be updated 30 Mar 2023 Jennifer Shelton 6747583da8c style: standardize whitespace 30 Mar 2023 Jennifer Shelton 924bb99b0dc feat: allow for input cram files that don't need to be updated 30 Mar 2023 Jennifer Shelton 8d27701dde1 feat: check regions per minute rate for a mutect2 log 28 Mar 2023 Timothy Chu f93f88d9dd0 M Pull request #2: update unique_bams.py and update_cram_info.py to new normalId tumorId naming Merge in WDL/somatic_dna_tools from tchu-dev to master
* commit '6983a84d2d018cf5560f8c053cccdaa38d6c20dc':
fix update_cram_info.py
update unique_bams.py to new normalId tumorId naming 13 Dec 2022 Timothy Chu 6983a84d2d0 fix update_cram_info.py 12 Dec 2022 Timothy Chu 88e5da233c2 update unique_bams.py to new normalId tumorId naming 12 Dec 2022 James Roche 355967b1015 M Pull request #1: feat: scripts to find unique bams for cram conversion task Merge in WDL/somatic_dna_tools from bam_to_cram to master
* commit 'd045787f68d8120908188edae24269b750d93c35':
feat: scripts to find unique bams for cram conversion task 31 May 2022 James Roche d045787f68d feat: scripts to find unique bams for cram conversion task 31 May 2022 Jennifer Shelton e837c6999b5 feat: add tools for pon workflow 29 Mar 2022 Jennifer Shelton 5d6fe740376 M Pull changes Merge branch 'master' of ssh://bitbucket.nygenome.org:7999/compbio/somatic_tools 14 Jan 2022 Jennifer Shelton 7f01e60b924 M pull online changes Merge branch 'master' of git.nygenome.org:compbio-pipelines/somatic_tools 14 Jan 2022 Jennifer Shelton 34a29a36629 feat: chrom filter added for vcf 14 Jan 2022 Jennifer Shelton ef47c0317e8 feat: pon tools added 14 Jan 2022 Jennifer Shelton f8fc13ccd45 feat: add deconstructsigs script to bitbucket repo 23 Nov 2021 Jennifer Shelton 823c6f443e7 refactor: gridss rearrangment to be clear about variable in command and allow call caching (by not using strings based on paths that change on runs)
and rearrange secondary preprocessing files so that gridss can find them
based on relative position 24 Aug 2021 
