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34 Open 101 Closed
34 Open 101 Closed
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Issues list

Saved input bams for MACS2?
#285 opened May 6, 2025 by bhanco
multiqc and dumpsoftwareversions not resumed bug Something isn't working
#283 opened Apr 14, 2025 by mirpedrol
Unexpected Inclusion of Bisulfite_Genome/ Files in Bowtie2 Alignment Step bug Something isn't working
#282 opened Apr 1, 2025 by edogiuili
JSON schema: Cutandrun documentation Improvements or additions to documentation
#280 opened Mar 25, 2025 by jen-reeve
6 of 15 tasks
@abartlett004
Could you please share the SVG file of the worflow subway diagram?
#278 opened Mar 13, 2025 by yinshiyi
implementation of fastp and implementation of extra trim arguments enhancement Improvement for existing functionality
#277 opened Mar 11, 2025 by sunta3iouxos
Strange error enhancement Improvement for existing functionality
#275 opened Feb 26, 2025 by stela2502
Understanding Spike-In Alignment Decisions
#274 opened Feb 10, 2025 by NikoBlank
2
Spikein and CPM normalization
#272 opened Jan 28, 2025 by aeeckhou
2
--save_reference does not save bowtie2 index bug Something isn't working
#270 opened Jan 22, 2025 by SuhasSrinivasan
4
Output Docs missing sections
#265 opened Nov 13, 2024 by JGroos-16
How to remove some chromosomes, e.g., chrUn_KI270438v1 bug Something isn't working
#264 opened Nov 12, 2024 by liuyang2006
uncommitted changed issue bug Something isn't working
#263 opened Oct 15, 2024 by dedeepyavaka
Multiple mapping parameters enhancement Improvement for existing functionality
#260 opened Oct 8, 2024 by KunFang93
Suggestion to implement "greenlist normalization" enhancement Improvement for existing functionality
#257 opened Sep 5, 2024 by GeroKn
@chris-cheshire
Is the default binsize really 1 when using CPM normalization? bug Something isn't working
#256 opened Aug 31, 2024 by nvictus
1
Process NFCORE_CUTANDRUN:CUTANDRUN:MULTIQC input file name collision bug Something isn't working
#255 opened Aug 30, 2024 by AprilJack
NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS terminated with an error exit status (137) pipeline_error
#254 opened Aug 20, 2024 by monovich
5
ERROR ~ ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist! pipeline_error
#253 opened Aug 7, 2024 by avanthikav
1
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)' pipeline_error
#252 opened Aug 7, 2024 by cutleraging
5
Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY (all_target_bams)': AttributeError: module 'matplotlib.cm' has no attribute 'register_cmap' pipeline_error
#251 opened Aug 7, 2024 by haipinghao
3
The AWS Access Key Id you provided does not exist in our records pipeline_error
#250 opened Aug 6, 2024 by cutleraging
2
PLOT_CONSENSUS_PEAKS worflow does not produce the upset plot bug Something isn't working WIP Work in progress
#248 opened Jul 24, 2024 by Alessandro201
3
Provide relative paths to resources in IGV session file bug Something isn't working feature-request Request for a new pipeline feature WIP Work in progress
#247 opened Jul 18, 2024 by siddharthab
2
How to set sample sheet without IgG control? question Further information is requested
#244 opened May 21, 2024 by yxralba088
3
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