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39 Open 124 Closed
39 Open 124 Closed
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Issues list

FastQC uses only 10 cores in a 32 core server enhancement New feature or request
#404 opened Jan 15, 2025 by SuhasSrinivasan
Please change default MACS2 peak calling to narrow peak enhancement New feature or request
#403 opened Jan 12, 2025 by SuhasSrinivasan
Issue when rerunning the pipeline for MACS2 narrow peak bug Something isn't working
#402 opened Jan 12, 2025 by SuhasSrinivasan
1
Pipeline fails quietly when input fastqs are not found bug Something isn't working
#401 opened Jan 11, 2025 by SuhasSrinivasan
Nextflow log does not show run time and status bug Something isn't working
#400 opened Jan 11, 2025 by SuhasSrinivasan
Allow discontinuing replicate numbers enhancement New feature or request
#397 opened Dec 19, 2024 by aghr
Compress deeptools .tab files and .fa genomes as they occupy a lot of space enhancement New feature or request
#395 opened Nov 28, 2024 by Alessandro201
Improve TRIMGALORE by adding pigz to Singularity container enhancement New feature or request
#394 opened Nov 27, 2024 by aghr
1
1
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:DOWNLOAD_SCOREFILES terminated with an error exit status (8)
#391 opened Nov 19, 2024 by vaksmaz
1
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
4
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
ProTip! no:milestone will show everything without a milestone.