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Issues list

DSL1: Typo in main.nf file bug Something isn't working
#1119 by Dog13Golf was closed Mar 21, 2025
@jfy133
2
utils_nf-core_eager_pipeline validation: Error expected but not raised in test datasets bug Something isn't working
#1114 by ilight1542 was closed Feb 14, 2025 3.0 Augsburg
@jfy133 @TCLamnidis @scarlhoff
4
DSL2: Sharding tweaks DSL2
#1104 by TCLamnidis was closed Feb 21, 2025
1
@jch-13
Unsupported class file major version 67 bug Something isn't working
#1097 by themudo was closed Oct 31, 2024
5 tasks done
1
DSL2: Ensure that all sharded fastQs make it into mapping. bug Something isn't working DSL2
#1089 by TCLamnidis was closed Jan 9, 2025 3.0 Augsburg
3
vcf2genome error bug Something isn't working
#1086 by dbajpp0 was closed Dec 20, 2024
3 tasks
1
DSL2 Metagenomics - Update the test-datasets and input-files for test profiles DSL2 small_fix
#1085 by merszym was closed Mar 25, 2025
1
@merszym @ilight1542
2
DSL2: Metagenomics: Allow Skip-pairmerging before running metagenomics DSL2 enhancement New feature or request
#1084 by merszym was closed Mar 25, 2025
@merszym @ilight1542
2
endorspy erroring in nf-core/ender workflow bug Something isn't working
#1083 by VerbalCant was closed Aug 20, 2024
5 tasks done
3
Add lane merging output directory to output documentation. bug Something isn't working DSL1
#1079 by TCLamnidis was closed Jun 28, 2024
1
MultiQC doesn't display post artrimming FASTQC results bug Something isn't working DSL1
#1073 by jfy133 was closed Jun 28, 2024
1
Use Sample-level merged BAMs for sample-level statistics bug Something isn't working DSL2
#1065 by TCLamnidis was closed Sep 20, 2024 3.0 Augsburg
1
@scarlhoff
1
CRAM output DSL2 enhancement New feature or request
#1059 by TCLamnidis was closed Dec 20, 2024
2
Input BAM files overwritten and emptied when using same filename as ID bug Something isn't working
#1051 by PCQuilis was closed Feb 21, 2024 2.5.1 - Bopfingen (patch)
1
1
Update eager version on figures to 2.5 DSL1
#1049 by TCLamnidis was closed Feb 9, 2024 2.5.1 - Bopfingen (patch)
1
1
Deprecate vcf2genome --vcf2genome_outfile parameter bug Something isn't working DSL1
#1048 by TCLamnidis was closed Feb 21, 2024 2.5.1 - Bopfingen (patch)
1
1
DSL1: Update multiqc clean_names to clean new names added in 2.5.0 bug Something isn't working DSL1
#1047 by TCLamnidis was closed Feb 21, 2024 2.5.1 - Bopfingen (patch)
1
1
DSL2: add test including bedtools BED file for feature stats bug Something isn't working
#1044 by jfy133 was closed Feb 2, 2024
5 tasks
1
DSL2: Add LB: to RG tags for all mappers DSL2 easier-tasks
#1042 by TCLamnidis was closed May 10, 2024 3.0 Augsburg
1
DSL2: 'single_end' and 'id_index' not present in meta of BAM input bug Something isn't working DSL2
#1040 by TCLamnidis was closed Mar 19, 2024 3.0 Augsburg
1
3
DSL2: Add library merge step after damage_manipulation DSL2
#1039 by TCLamnidis was closed Mar 18, 2024 3.0 Augsburg
1
1
bedtools coverage fails when gff file and genome file are not sorted the same way bug Something isn't working
#1037 by IdoBar was closed Feb 21, 2024
5 tasks done
2.5.1 - Bopfingen (patch)
1
1
DSL2: add circularmapper module DSL2 enhancement New feature or request
#1033 by shyama-mama was closed Aug 16, 2024 3.0 Augsburg
@shyama-mama
3
DSL1: No fasta indexing when using bowtie2. bug Something isn't working DSL1
#1031 by TCLamnidis was closed Nov 7, 2023
2 of 5 tasks
1
DSL2: add reference masking for PMDtools enhancement New feature or request
#1029 by scarlhoff was closed Dec 12, 2023
1
@scarlhoff
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