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Issues: uclahs-cds/pipeline-align-DNA

Input csv fields: redundancy ok?
#143 opened Oct 22, 2021 by alkaZeltser
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25 Open 117 Closed
25 Open 117 Closed
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Issues list

Apply methods.setup_process_afterscript() for all processes
#329 opened Jul 1, 2024 by yashpatel6
@j2salmingo
sort BWA-MEM output directly avoiding intermediate write step
#315 opened May 20, 2024 by sorelfitzgibbon
Potentially serious problem with read group definitions high priority high priority issues
#308 opened Apr 25, 2024 by sorelfitzgibbon
5
Update repository description to match standard standardization
#306 opened Apr 11, 2024 by nwiltsie
BAM Filename standardization for alignment pipelines
#293 opened Jan 26, 2024 by yashpatel6
Update default reference path (alt-aware reference) in template config high priority high priority issues
#281 opened Nov 14, 2023 by tyamaguchi-ucla
@yashpatel6 @j2salmingo
1
Compare scratch usage between MarkDuplicatesSpark and SAMtools markdup enhancement New feature or request
#278 opened Oct 3, 2023 by tyamaguchi-ucla
@yashpatel6 @j2salmingo
2
Config file generation script is out of date for v9.0.0 bug Something isn't working documentation Improvements or additions to documentation
#276 opened Aug 9, 2023 by j2salmingo
Adding fastp as a configurable option enhancement New feature or request
#272 opened Jul 5, 2023 by raagagrawal
@yashpatel6
1
No error during align-DNA failure
#252 opened Dec 6, 2022 by alkaZeltser
@jarbet
7
Process inclusion warnings
#251 opened Dec 1, 2022 by yashpatel6
@jarbet
Change check_512sum to use PipeVal enhancement New feature or request
#244 opened Sep 28, 2022 by jarbet
@jarbet
Replace docker validate with pipeline-Nextflow-module validate enhancement New feature or request
#239 opened Aug 31, 2022 by jarbet
1
@jarbet
Run MarkDuplicatesSpark by library enhancement New feature or request
#234 opened Aug 8, 2022 by tyamaguchi-ucla
@j2salmingo
4
run_MarkDuplicatesSpark_GATK error exit status (3) with CPCG0196-F1
#229 opened Jul 29, 2022 by jarbet
@tyamaguchi-ucla @yashpatel6 @jarbet
8
Parameterize --VALIDATION_STRINGENCY enhancement New feature or request Task
#224 opened Jul 24, 2022 by tyamaguchi-ucla
@jarbet
GATK's MarkDuplicatesSpark outputs and empty bam file for an ICGC cohort of WGS FASTQs blocked Work on this issue cannot proceed because another issue must be closed first bug Something isn't working
#223 opened Jul 23, 2022 by Alfredo-Enrique
@tyamaguchi-ucla @yashpatel6 @jarbet
24
Runs fail because not enough memory for MarkDuplicates | How much memory should I give it?
#221 opened Jul 20, 2022 by Alfredo-Enrique
@tyamaguchi-ucla @yashpatel6 @jarbet
9
temp dir standardization (low priority)
#183 opened Mar 22, 2022 by tyamaguchi-ucla
Invalid hisat alignments with new genome
#165 opened Jan 19, 2022 by aakarsh-anand
Different genomes for BWA-MEM2 and HISAT2
#147 opened Nov 8, 2021 by tyamaguchi-ucla
Input csv fields: redundancy ok? question Further information is requested
#143 opened Oct 22, 2021 by alkaZeltser
@tyamaguchi-ucla
5
Centralize config generation in PR #116 for use in other pipelines
#118 opened Jun 16, 2021 by aholmes
Add option to build hisat2 index to generate-genome-index.nf enhancement New feature or request
#114 opened Jun 7, 2021 by aakarsh-anand
Change the behavior node configuration and dynamic resource allocation enhancement New feature or request
#56 opened Feb 11, 2021 by aholmes
@zhuchcn
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