Issues

• DSL2 port?

  enhancement
  nf-core/clipseq#180 · Filter by author grexor opened on Sep 18, 2026

• feat-2-0: Unknown config attribute params.fastq

  bug
  nf-core/clipseq#177 · Filter by author slebedeva opened on Feb 6, 2026

• feat2-0, no concatenation of fastqs

  bug
  nf-core/clipseq#176 · Filter by author MartiPedna opened on Dec 2, 2025
  1

• iGenomes GRCh37 misread (?) during pureclip peakcalling

  bug
  nf-core/clipseq#173 · Filter by author irikas opened on Nov 13, 2025

• No compatible iGenomes genome for iCount peakcaller

  bug
  nf-core/clipseq#172 · Filter by author irikas opened on Nov 13, 2025

• Create new test data

  enhancement
  nf-core/clipseq#171 · Filter by author Chromojones opened on Nov 10, 2025

• we need minus bigwig with positive signal

  bug
  nf-core/clipseq#170 · Filter by author CharlotteAnne opened on Nov 10, 2025
  

• iCount summaries error

  bug
  nf-core/clipseq#168 · Filter by author iraiosub opened on Jun 12, 2025

• Crosslinks and peaks are not produced for all samples in the samplesheet

  bug
  Bug

  nf-core/clipseq#167 · Filter by author kkuret opened on May 18, 2025
  1

  

• Add promoter, enhancer annotations to regional summaries from genehancer for organisms where this is available

  enhancement
  nf-core/clipseq#164 · Filter by author CharlotteAnne opened on Apr 4, 2025

• document the annotation options and outputs

  enhancement
  Task

  nf-core/clipseq#163 · Filter by author iraiosub opened on Mar 28, 2025
  

• Remove the separate filer_gtf module that filters for Ensembl_canonical flag

  enhancement
  nf-core/clipseq#157 · Filter by author kkuret opened on Mar 26, 2025

• rename longest_transcript-related params and outputs more meaningfully

  enhancement
  Task

  nf-core/clipseq#156 · Filter by author iraiosub opened on Mar 26, 2025
  

• When transcript filtering is applied to GTF, the selected transcripts should also be used for transcriptome analyses

  enhancement
  nf-core/clipseq#141 · Filter by author kkuret opened on Mar 25, 2025

• make filtering the GTF and downstream steps optional

  enhancement
  nf-core/clipseq#140 · Filter by author iraiosub opened on Mar 24, 2025
  

• write subworkflow

  enhancement
  nf-core/clipseq#138 · Filter by author MelinaKlostermann opened on Mar 24, 2025
  

• Test and integarte peak input from peakcallers other then pureclip

  enhancement
  nf-core/clipseq#137 · Filter by author MelinaKlostermann opened on Mar 24, 2025

• tube map diagram!

  enhancement
  nf-core/clipseq#132 · Filter by author CharlotteAnne opened on Mar 21, 2025

• update pipeline to latest nf-core template

  enhancement
  nf-core/clipseq#131 · Filter by author CharlotteAnne opened on Mar 21, 2025

• update all nf-core modules

  enhancement
  nf-core/clipseq#130 · Filter by author CharlotteAnne opened on Mar 21, 2025
  1

• create QC report module

  enhancement
  nf-core/clipseq#127 · Filter by author CharlotteAnne opened on Mar 18, 2025
  

• add ucsc bedgraph->bigwig to pipeline as BSF input

  enhancement
  nf-core/clipseq#126 · Filter by author CharlotteAnne opened on Mar 18, 2025
  1

  

• add into main pipeline

  enhancement
  nf-core/clipseq#125 · Filter by author CharlotteAnne opened on Mar 18, 2025
  1

  

• adding nf-test to CI workflow

  enhancement
  nf-core/clipseq#124 · Filter by author CharlotteAnne opened on Mar 18, 2025

• nf-test

  enhancement
  nf-core/clipseq#123 · Filter by author CharlotteAnne opened on Mar 18, 2025