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30 Open 123 Closed
30 Open 123 Closed
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Issues list

Sorting bedgraph using gnu sort instead of bedtools sort
#390 opened Nov 4, 2024 by johapark
Latest version still generated MACS2, not MACS3 bug Something isn't working
#389 opened Nov 2, 2024 by liuyang2006
1
Scale bar inconsistency across samples enhancement New feature or request
#388 opened Oct 31, 2024 by hyjforesight
Set chromap to not shift reads by default enhancement New feature or request
#381 opened Sep 27, 2024 by JoseEspinosa 2.2
@JoseEspinosa
ATAC-seq Spike-in control enhancement New feature or request
#380 opened Sep 23, 2024 by whw006
Picard "--TMP_DIR" arguments are hardcoded bug Something isn't working
#378 opened Aug 16, 2024 by vondoRishi
ERROR ~ Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE bug Something isn't working
#377 opened Aug 10, 2024 by Kermaa
AttributeError: module 'matplotlib.cm' has no attribute 'register_cmap' bug Something isn't working
#376 opened Jul 15, 2024 by kasiabla
2
New release please? enhancement New feature or request
#373 opened Jul 4, 2024 by siddharthab
1
Feature Request: call peaks for each replicate (diffbind), not only the merged data enhancement New feature or request
#367 opened Jun 28, 2024 by lindenb
3
deprecated container formats bug Something isn't working
#361 opened Apr 8, 2024 by LinearParadox
@JoseEspinosa
1
suggestion: use samtools view --uncompressed before piping in bamtools_filter enhancement New feature or request
#346 opened Jan 26, 2024 by lindenb
Feature Request: summary table for each sample enhancement New feature or request
#345 opened Jan 26, 2024 by lindenb
1
bam_csi_index parameter for ATACSeq enhancement New feature or request
#343 opened Dec 20, 2023 by BianyunY-ACRD
implement the bam_csi_index parameter in atacseq pipeline enhancement New feature or request
#340 opened Oct 27, 2023 by BianyunY-ACRD
Process terminated for an unknown reason (SLURM) bug Something isn't working
#339 opened Oct 16, 2023 by hdbeukel
1
the sample field from the samplesheet is too lenient bug Something isn't working WIP Work in progress
#338 opened Oct 9, 2023 by maxulysse
@JoseEspinosa
MAKE_GENE_BED making 0kb .bed files
#334 opened Sep 6, 2023 by hcliedtke
CSI bam index not working bug Something isn't working
#327 opened Aug 10, 2023 by heathfuqua
1
1
Add GRCm39 option to config enhancement New feature or request
#273 opened May 2, 2023 by laurenhsu1
1
Biotype analysis using featureCounts enhancement New feature or request
#188 opened Aug 11, 2022 by chuan-wang
Peak calling parameters might not be ideal enhancement New feature or request
#169 opened Feb 17, 2022 by ktrns
3
Genome annotation (gene names) missing in IGV session file enhancement New feature or request
#168 opened Feb 17, 2022 by ktrns
1
Does nf-core/atacseq apply an offset to each ATAC-seq fragment? question Further information is requested
#164 opened Sep 22, 2021 by rcorces 2.0
3
Addition of peak-calling with Genrich enhancement New feature or request
#108 opened Jun 13, 2020 by chlazaris 2.2
@i-pletenev @samuelruizperez
ProTip! What’s not been updated in a month: updated:<2024-10-10.