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45 Open 378 Closed
45 Open 378 Closed
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Issues list

DSL2: Add 'output' documention for mtnucratio documentation DSL2
#1070 opened May 17, 2024 by scarlhoff
DSL2: Add MultiVCFAnalyzer DSL2 enhancement New feature or request
#1069 opened May 17, 2024 by aidaanva
@aidaanva
DSL2: Ensure modules config consistency: all modules have an ext.prefix and publishDir attribute, and follow conventions. DSL2
#1066 opened Apr 26, 2024 by TCLamnidis 3.0 Augsburg
Use Sample-level merged BAMs for sample-level statistics bug Something isn't working DSL2
#1065 opened Apr 26, 2024 by TCLamnidis 3.0 Augsburg
1
CRAM output DSL2 enhancement New feature or request
#1059 opened Mar 22, 2024 by TCLamnidis
1
Fix description of mt/n ratio in docs documentation DSL2
#1055 opened Feb 28, 2024 by TCLamnidis 3.0 Augsburg
Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed DSL2
#1054 opened Feb 23, 2024 by TCLamnidis
DSL2: add circularmapper module DSL2 enhancement New feature or request
#1033 opened Nov 3, 2023 by shyama-mama 3.0 Augsburg
@shyama-mama
3
DSL2: Allow changing parameters for BWA mem. DSL2 enhancement New feature or request
#1026 opened Oct 19, 2023 by TCLamnidis
DSL2: Add HapCON? DSL2 enhancement New feature or request
#1015 opened Jul 21, 2023 by TCLamnidis
DSL2: Add to MultiQC support for coverage_across_reference.txt file enhancement New feature or request
#1001 opened Jun 23, 2023 by jfy133
DSL2: BAM to FastQ conversion. Ensure that lane info is kept. DSL2
#999 opened Jun 9, 2023 by TCLamnidis 3.0 Augsburg
@jfy133
DSL2: Print Nuclear Contamination JSON N/A value bug Something isn't working DSL2
#995 opened Jun 7, 2023 by TCLamnidis 3.0 Augsburg
2
DSL2: Ensure to document input run BAMs will _not_ be merged with FASTQ libraries even if same name DSL2 enhancement New feature or request
#994 opened Jun 2, 2023 by jfy133 3.0 Augsburg
2
DSL2: PMDTools for estimation vs manipulation of damage DSL2
#989 opened May 26, 2023 by TCLamnidis
DSL2: Add input BAM BAM2FASTQ conversion support for remapping DSL2 enhancement New feature or request
#987 opened May 26, 2023 by jfy133 3.0 Augsburg
@jfy133
DSL2: Add test profile that forces ALL the possible merging steps for FastQ and BAM inputs, to ensure no file name collisions happen. DSL2
#986 opened May 25, 2023 by TCLamnidis 3.0 Augsburg
DSL2: Add lane attribute to BAM inputs bug Something isn't working DSL2
#985 opened May 25, 2023 by TCLamnidis
3 tasks
3.0 Augsburg
@jfy133
DSL2: ensure versions.yml aren't published DSL2 enhancement New feature or request
#979 opened May 11, 2023 by scarlhoff 3.0 Augsburg
1
DSL2: Provide correct data for upload to sequencing archives (e.g. ENA) DSL2 enhancement New feature or request
#974 opened May 2, 2023 by TCLamnidis 3.0 Augsburg
DSL2L: Add support for specifying platform in input TSV DSL2 enhancement New feature or request
#970 opened Apr 21, 2023 by jfy133 3.0 Augsburg
DSL2: Make publication of large intermediate files opt-in DSL2 enhancement New feature or request
#968 opened Mar 31, 2023 by scarlhoff
Possiblity to extract non-host paired-end reads in separate FastQ files DSL2 enhancement New feature or request
#945 opened Feb 22, 2023 by alexhbnr 3.0 Augsburg
@jfy133
DSL2: Document loudly that -params-files should replace custom.config for parameters DSL2 enhancement New feature or request
#943 opened Jan 25, 2023 by jfy133 3.0 Augsburg
subset large datasets for dataset-wide statistics DSL2
#942 opened Jan 5, 2023 by ChristopherBarrington 3.0 Augsburg
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