Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / broadinstitute/gatk-for-microbes issues and pull requests

#30 - Status?

Issue - State: open - Opened by knokknok about 1 year ago - 1 comment

#30 - Status?

Issue - State: open - Opened by knokknok about 1 year ago - 1 comment

#29 - Docker independent pipeline?

Issue - State: open - Opened by Guan06 over 2 years ago - 2 comments

#29 - Docker independent pipeline?

Issue - State: open - Opened by Guan06 over 2 years ago - 2 comments

#28 - test script fails because ShiftFasta command is missing

Issue - State: open - Opened by kxw116 over 3 years ago - 1 comment

#28 - test script fails because ShiftFasta command is missing

Issue - State: open - Opened by kxw116 over 3 years ago - 1 comment

#26 - Skip revertsam and samtofastq when the input is bam file

Issue - State: closed - Opened by bhanugandham almost 4 years ago

#26 - Skip revertsam and samtofastq when the input is bam file

Issue - State: closed - Opened by bhanugandham almost 4 years ago

#25 - Script for merging bed files

Pull Request - State: closed - Opened by sophiegr02 almost 4 years ago

#25 - Script for merging bed files

Pull Request - State: closed - Opened by sophiegr02 almost 4 years ago

#23 - added gatk-microbial jar and shiftfasta jars to input json

Pull Request - State: closed - Opened by bhanugandham almost 4 years ago

#23 - added gatk-microbial jar and shiftfasta jars to input json

Pull Request - State: closed - Opened by bhanugandham almost 4 years ago

#22 - How to build gatk-micobialmode.jar?

Issue - State: closed - Opened by garlandcrow almost 4 years ago - 4 comments

#22 - How to build gatk-micobialmode.jar?

Issue - State: closed - Opened by garlandcrow almost 4 years ago - 4 comments

#21 - test with recover-all-branches M2 arg

Issue - State: open - Opened by bhanugandham almost 4 years ago

#21 - test with recover-all-branches M2 arg

Issue - State: open - Opened by bhanugandham almost 4 years ago

#20 - Rosalind exercises to be reviewed

Pull Request - State: closed - Opened by sophiegr02 almost 4 years ago

#20 - Rosalind exercises to be reviewed

Pull Request - State: closed - Opened by sophiegr02 almost 4 years ago

#19 - remove the hard coded override for shift fasta

Pull Request - State: closed - Opened by ahaessly about 4 years ago

#19 - remove the hard coded override for shift fasta

Pull Request - State: closed - Opened by ahaessly about 4 years ago

#18 - added wdl to generate frequency of zmw occurances

Pull Request - State: closed - Opened by bhanugandham about 4 years ago

#18 - added wdl to generate frequency of zmw occurances

Pull Request - State: closed - Opened by bhanugandham about 4 years ago

#17 - Ah shift bool

Pull Request - State: closed - Opened by ahaessly about 4 years ago

#17 - Ah shift bool

Pull Request - State: closed - Opened by ahaessly about 4 years ago

#16 - Exclude the filtered variants from the filtered.vcf output file

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: bug

#16 - Exclude the filtered variants from the filtered.vcf output file

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: bug

#15 - Add a task for Terra UI to hide optional json outputs

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: stretch goals

#15 - Add a task for Terra UI to hide optional json outputs

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: stretch goals

#14 - Explain the three output bamouts in documentation

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: documentation

#14 - Explain the three output bamouts in documentation

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: documentation

#13 - Make shift fasta optional

Issue - State: closed - Opened by bhanugandham about 4 years ago
Labels: enhancement

#13 - Make shift fasta optional

Issue - State: closed - Opened by bhanugandham about 4 years ago
Labels: enhancement

#12 - Add an option in the wdl to prefix output files with sample_name

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: enhancement

#12 - Add an option in the wdl to prefix output files with sample_name

Issue - State: open - Opened by bhanugandham about 4 years ago
Labels: enhancement

#11 - Add joint calling as an option to the pipeline

Issue - State: open - Opened by bhanugandham about 4 years ago - 1 comment
Labels: enhancement

#11 - Add joint calling as an option to the pipeline

Issue - State: open - Opened by bhanugandham about 4 years ago - 1 comment
Labels: enhancement

#10 - Generate RTG vcfeval summary.txt file as an output concordance wdl

Issue - State: open - Opened by bhanugandham about 4 years ago - 1 comment
Labels: bug

#9 - Revert "add flag for circular reference (#8)"

Pull Request - State: closed - Opened by bhanugandham about 4 years ago - 1 comment

#8 - add flag for circular reference

Pull Request - State: closed - Opened by ahaessly about 4 years ago

#7 - Ah fix bamout

Pull Request - State: closed - Opened by ahaessly about 4 years ago

#6 - Ah concordance

Pull Request - State: closed - Opened by ahaessly over 4 years ago

#5 - adding run date readgroup

Pull Request - State: closed - Opened by bhanugandham over 4 years ago

#4 - wdl for RTG comparison

Pull Request - State: closed - Opened by ahaessly over 4 years ago

#3 - added bamout to inputs json and removed the max-mnp-distance argument

Pull Request - State: closed - Opened by bhanugandham over 4 years ago

#2 - Bg add bamout

Pull Request - State: closed - Opened by bhanugandham over 4 years ago

#1 - Ah- initial wdl

Pull Request - State: closed - Opened by ahaessly over 4 years ago