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Installfix#26

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attilagk wants to merge 189 commits intobsmn:masterbsmn/bsmn-pipeline:masterfrom attilagk:installfixattilagk/bsmn-pipeline:installfixCopy head branch name to clipboard

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Commits on Jan 20, 2018

• Create README.md

  bintriz

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• Minor fix.

  

  cfncluster user

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• Edit README.

  

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Commits on Feb 14, 2018

• a small change in removing files.

  

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• Adjust the threaded option.

  

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• Add an analysis script caculating VAF.

  

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• Add nda related utils.

  

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Commits on Feb 19, 2018

• Add a script for strand bias analysis.

  

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Commits on Feb 21, 2018

• Change VAF script.

  

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• Refactoring.

  

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Commits on Feb 22, 2018

• Bug fix: import sys was omitted.

  

  cfncluster user

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Commits on Feb 24, 2018

• Change p-val format into scientific notation.

  

  cfncluster user

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Commits on Apr 16, 2018

• Change binomial test into one-sided (smaller).

  

  cfncluster user

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Commits on Jun 17, 2018

• Move library location.

  bintriz

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• Add germline_filter.py

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Commits on Jun 29, 2018

• Change germline filter script

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Commits on Jun 30, 2018

• change location of the library and conf file in genome mapping pipeline

  bintriz

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• change library/job_queue.py location

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Commits on Jul 11, 2018

• Add configurations for root and cnvnator.

  bintriz

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• Add variant_calling pipeline.

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Commits on Aug 21, 2018

• find samtools path when config not working

  

  [email protected]

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Commits on Oct 1, 2018

• Add missing variable.

  bintriz

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• Create requirements.txt

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  Kenneth Daily

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• Update requirements.txt

  

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• Update README.md

  

  Kenneth Daily

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• Update README.md

  

  Kenneth Daily

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• Update README.md

  

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Commits on Oct 19, 2018

• Bug fix.

  bintriz

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• Add an automatic tool installer.

  bintriz

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• Merge pull request bsmn#8 from bsmn/kdaily-add-py-requirements

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• Merge pull request bsmn#9 from bsmn/kdaily-add-contrib

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• Merge pull request bsmn#10 from bsmn/kdaily-add-setup-notes

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• Merge branch 'master' of github.com:bsmn/bsmn_pipeline

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• Merge pull request bsmn#13 from bsmn/tool_installer

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Commits on Nov 24, 2018

• Bug fix: install_tools.sh

  bintriz

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• Add a script for resource download

  bintriz

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Commits on Nov 25, 2018

• Change configuration system

  bintriz

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• pileup.py upadte as configuration system changes

  bintriz

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Commits on Nov 26, 2018

• synpase_login refactoring

  bintriz

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• Add nda_login

  bintriz

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• Refactoring: config, run_info

  bintriz

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• Library name change: utils -> misc

  bintriz

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• Refactoring sample list parser & Fix sample list format

  bintriz

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• Add synapse login in the download_resources.sh

  bintriz

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  1a8c017

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• Add NDA download funtion

  bintriz

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• Minor change in job scripts

  bintriz

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• Refactoring: rename analysis_utils -> utils

  bintriz

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Commits on Nov 28, 2018

• Add an option for turning off bam upload to synapse

  bintriz

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• Add wrapper scripts for pipeline runners

  bintriz

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  aad38a2

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• Bug_fix: NDA credential setting

  bintriz

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  2818e1c

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• minor change of the argument help in runners

  bintriz

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  9675dea

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• Simplify aws download log

  bintriz

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• Removing a conflict of tmp collate file names when running bam2fq on multiple bams

  bintriz

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Commits on Dec 4, 2018

• Refactoring: run_info, log_dir

  bintriz

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• Change location to save run_info

  bintriz

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• Improve error handling in job_scripts

  bintriz

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• Add user's S3Uri and LocalPath options for data source; Multiple try when downloading data

  bintriz

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• Bug fix: Not updating the return code of multiple download tries

  bintriz

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• Bug fix: Make sample dir before saving run_info

  bintriz

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Commits on Dec 5, 2018

• Adjust threaded and java Xmx to match with m5.12xlarge

  bintriz

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Commits on Dec 9, 2018

• Java memory adjustment

  bintriz

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Commits on Dec 10, 2018

• Update the README file

  bintriz

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• Update the README file

  bintriz

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  69347c5

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• Merge pull request bsmn#14 from bsmn/bug_fix

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  Kenneth Daily

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• Merge pull request bsmn#15 from bsmn/pull-request-tj-update

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  Kenneth Daily

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Commits on Jan 15, 2019

• Small edits on README.md

  attilagk

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• Merge pull request bsmn#16 from attilagk/edits

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  bintriz

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• install_tools.sh now downloads and extracts GATK

  attilagk

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• Removed manual download of GATK from README.md

  attilagk

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Commits on Jan 16, 2019

• Merge pull request bsmn#17 from attilagk/edits

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• Recommended install location in README.md

  attilagk

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Commits on Apr 30, 2019

• Bug fix:NDA api url change

  bintriz

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• Bug fix:sample list input parser change

  bintriz

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• Add templates for new job scripts

  bintriz

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• Small change PON filter

  bintriz

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• Merge pull request bsmn#22 from bsmn/pull-request-tj-update

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  Kenneth Daily

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Commits on May 6, 2019

• Add mutect2 single sample workflow

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  sean-cho

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• Update resources

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  sean-cho

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Commits on May 8, 2019

• Merge pull request bsmn#23 from sean-cho/scho-updates

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  bintriz

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Commits on May 15, 2019

• add alt_bq_sum.py with modification of pileup library

  bintriz

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Commits on May 28, 2019

• bug fix: pileup

  bintriz

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Commits on May 29, 2019

• update

  douym

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Commits on Jun 4, 2019

• update

  douym

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Commits on Jun 18, 2019

• Merge pull request bsmn#18 from attilagk/master

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  bintriz

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• Update README.md

  bintriz

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• Update the root and cnvnator part of the install script

  bintriz

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• Merge branch 'master' of https://github.com/bsmn/bsmn_pipeline

  bintriz

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Commits on Jul 31, 2019

• Merge pull request bsmn#24 from douym/douym-update-install

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  bintriz

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Commits on Aug 1, 2019

• Fix: root installation

  bintriz

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• Merge branch 'master' of https://github.com/bsmn/bsmn_pipeline

  bintriz

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Commits on Aug 2, 2019

• Remove conda dependendy in installing the depending tools of MosaicForecast

  bintriz

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Commits on Aug 3, 2019

• Add codes installing RetroSom dependencies

  bintriz

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Commits on Aug 10, 2019

• Modify to skip installing installed tools

  bintriz

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Commits on Aug 12, 2019

• Update README.md

  bintriz

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Commits on Aug 14, 2019

• Separate filtering steps from calling.

  bintriz

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• Remove template job scripts not in use

  bintriz

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• Rename the cnvnator job script

  bintriz

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• Change output directory structure & disable indel quals and original quals from the bqsr step

  bintriz

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• Add cram conversion step

  bintriz

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• Add a step extracting unmapped reads

  bintriz

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  7a58a0c

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• Add mutect-sinle job scripts

  bintriz

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• Add a job submitter for mutect-single

  bintriz

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• Add new gatk hc job scripts implemented using gatk4

  bintriz

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• Create a new job submitter to separate gatk-hc by copying run.py

  bintriz

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• Merge branch 'master' of https://github.com/bsmn/bsmn_pipeline

  bintriz

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Commits on Aug 17, 2019

• Fix a typo

  bintriz

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• Rename run_aln_jobs

  bintriz

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• Add MASTER_SERVER into run_info

  bintriz

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• Change the final file format of output from bam to cram

  bintriz

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Commits on Aug 18, 2019

• Rollback file names: submit_aln_jobs

  bintriz

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• Reflect the rollback of submit_aln_jobs

  bintriz

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  b466ec4

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• Change upload logic. Allow to run genome mapping together with variant calling.

  bintriz

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• Bug fix

  bintriz

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Commits on Aug 19, 2019

• Change the alignment working directory from bam to alignment

  bintriz

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• Change java path

  bintriz

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Commits on Aug 20, 2019

• Update wrapper scripts

  bintriz

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  a49dd77

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• Rename wrapper scripts

  bintriz

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  e250db8

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• Remove blank lines in run_info

  bintriz

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  88d921d

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• Bug fix: download script

  bintriz

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  4b69ff7

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• Reorganize job files & some bug fixes

  bintriz

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  7ab9ed5

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• Bug fixes: wrong variable names

  bintriz

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Commits on Aug 25, 2019

• Bug fix: GATK-HC jobs

  bintriz

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• Rearrange job orders

  bintriz

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Commits on Aug 27, 2019

• Bug fix: upload_cram

  bintriz

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Commits on Aug 28, 2019

• Add run_jid to track submitted jids

  bintriz

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Commits on Aug 29, 2019

• Add the feature stamping run_status when finishing a job

  bintriz

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Commits on Aug 31, 2019

• Bug fix: run_status stamp

  bintriz

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• Add a feature of skipping to submit jobs for already running samples

  bintriz

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• Change in printing maessage

  bintriz

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Commits on Sep 3, 2019

• Better logging for the download job

  bintriz

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• Add the limit of concurrent download jobs

  bintriz

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Commits on Sep 6, 2019

• Add con-down-limit

  bintriz

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  ad0d0e5

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• Fix bug: Skipping jobs for gatk-hc ploidy_12,50

  bintriz

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• Bug fix: symbolic link problem when running in a local cluster

  bintriz

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Commits on Sep 9, 2019

• Bug fix: ssh StricHostKeyChecking option in the jobs of submitting other jobs

  bintriz

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• Bug fix: run ssh excute remote commands as a login shell

  bintriz

  committed
  2ab14a6

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• Turn on the rerun otpion (-r y) of all jobs

  bintriz

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• Change threaded option for downloading

  bintriz

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Commits on Sep 12, 2019

• Bug fix: aln_2.merge error when reruning it

  bintriz

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• Bug fix: Add a feature of deleting failed download files

  bintriz

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  717933b

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• Adjust thread num in download job

  bintriz

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• Adjust default con-down-limit value according to the thread num of the download job

  bintriz

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• Increase the java memeory of the markdup job

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Commits on Sep 20, 2019

• Add trap in gatk-hc jobs

  bintriz

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• Bug fix: correct log messages of aln_5.bqsr.sh

  bintriz

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Commits on Sep 21, 2019

• gatk-hc vqsr: increase the parameter of maxum-training-variants to 5000000

  bintriz

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Commits on Oct 7, 2019

• Bug fix: duplicate jobs in running when the pre_2.submit_aln_jobs.sh is resubmitted.

  bintriz

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• Separate checkpoint per each step in a same job.

  bintriz

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Commits on Oct 9, 2019

• Incorporating bam2cram conversion steps to variant calling.

  bintriz

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Commits on Oct 10, 2019

• Bug fix

  bintriz

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• Bug fix: wrong bash variable name

  bintriz

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• Bug fix & refactoring of run_genome_mapping.py

  bintriz

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Commits on Oct 11, 2019

• Bug fix: Specify tmp path in bam2cram

  bintriz

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• Remove the existing sam when bam2cram starts

  bintriz

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• Add a new script that monitoring and resubmitting hanging jobs in queue

  bintriz

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Commits on Oct 18, 2019

• Change the logic of split fq files per lane: processing files by R1 and R2

  bintriz

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Commits on Nov 14, 2019

• Change Picard version 2.17.4 for error correction

  bintriz

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• Minor fix in log output

  bintriz

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  2a2b3ec

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• Bug fix in the mapping job submitter

  bintriz

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• Bug fix: creating tmp directory which running variant calling jobs only

  bintriz

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• Bug fix: no bai file of the merge bam when only one read group exists

  bintriz

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• Bug fix: error in markdup due to not enough tmp space

  bintriz

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Commits on Nov 18, 2019

• Bug fix: flagstat isn't excuted

  bintriz

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Commits on Dec 3, 2019

• Add a python util for calculating STR info

  bintriz

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Commits on Dec 27, 2019

• Bug fix: changing regex for grabbing fastq file name

  bintriz

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  a9b6b84

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• Increasing the max bam file size to handle up to 2TB

  bintriz

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  e3f0c1e

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• Merge branch 'master' of https://github.com/bsmn/bsmn-pipeline

  bintriz

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Commits on Mar 11, 2020

• downloaded archived tools

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Commits on Mar 17, 2020

• Downloads to synapse started

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• downloads upload to synapse now works; TODO: documentation

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• downloads to synapse script documented

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Commits on Mar 18, 2020

• added diagnostic status messages

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• fixing install_tools.sh

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• removed Python3 and pip installation from install_tools.sh

  

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Commits on Mar 19, 2020

• installfix in progress

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• completed install_tools.sh fix; some tools could not be fixed

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• zlib to install_tools

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• Made download_resources.sh more efficient and simple

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Commits on Mar 20, 2020

• started documenting the installfix branch

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Commits on Mar 21, 2020

• updated README.md with Versions section

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Commits on Mar 23, 2020

• Fixed misformatting in README

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Commits on Mar 25, 2020

• adding tests directory

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Commits on Mar 26, 2020

• removed duplicate args to pip

  

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Commits on Apr 1, 2020

• updated config.read function with tools not installed under bsmn-pipeline

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Commits on Apr 6, 2020

• cython installation is added to install_tools

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Commits on Apr 8, 2020

• quick fix for config allowed mapping to run down to aln_1.align_sort.sh

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Commits on Apr 13, 2020

• mapping ran until indel realignment

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Commits on Apr 16, 2020

• NDAR credentials to be modified

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Commits on Apr 20, 2020

• fixing path to awscli

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