nf-core/clipseq

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CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

Stars: 26
Forks: 43
Open beginner issues: 0
Indexed issues: 43

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 28, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

43 open issues indexed

DSL2 port? Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/clipseq#180 · Opened Sep 18, 2026
feat-2-0: Unknown config attribute params.fastq Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 50/100

nf-core/clipseq#177 · Opened Feb 6, 2026
feat2-0, no concatenation of fastqs Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/clipseq#176 · 1 comment · Opened Dec 2, 2025
iGenomes GRCh37 misread (?) during pureclip peakcalling Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/clipseq#173 · Opened Nov 13, 2025
No compatible iGenomes genome for iCount peakcaller Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/clipseq#172 · Opened Nov 13, 2025
Create new test data Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/clipseq#171 · Opened Nov 10, 2025
we need minus bigwig with positive signal Open

bug

nf-core/clipseq#170 · 1 assignee · Opened Nov 10, 2025
iCount summaries error Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/clipseq#168 · Opened Jun 12, 2025
Crosslinks and peaks are not produced for all samples in the samplesheet Open

bug

nf-core/clipseq#167 · 1 comment · 1 assignee · Opened May 18, 2025
Add promoter, enhancer annotations to regional summaries from genehancer for organisms where this is available Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/clipseq#164 · Opened Apr 4, 2025
document the annotation options and outputs Open

enhancement

nf-core/clipseq#163 · 1 assignee · Opened Mar 28, 2025
Remove the separate filer_gtf module that filters for Ensembl_canonical flag Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/clipseq#157 · Opened Mar 26, 2025
rename longest_transcript-related params and outputs more meaningfully Open

enhancement

nf-core/clipseq#156 · 1 assignee · Opened Mar 26, 2025
When transcript filtering is applied to GTF, the selected transcripts should also be used for transcriptome analyses Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/clipseq#141 · Opened Mar 25, 2025
make filtering the GTF and downstream steps optional Open

enhancement

nf-core/clipseq#140 · 1 assignee · Opened Mar 24, 2025
write subworkflow Open

enhancement

nf-core/clipseq#138 · 1 assignee · Opened Mar 24, 2025
Test and integarte peak input from peakcallers other then pureclip Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/clipseq#137 · Opened Mar 24, 2025
tube map diagram! Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/clipseq#132 · Opened Mar 21, 2025
update pipeline to latest nf-core template Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/clipseq#131 · Opened Mar 21, 2025
update all nf-core modules Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/clipseq#130 · 1 comment · Opened Mar 21, 2025
create QC report module Open

enhancement

nf-core/clipseq#127 · 1 assignee · Opened Mar 18, 2025
add ucsc bedgraph->bigwig to pipeline as BSF input Open

enhancement

nf-core/clipseq#126 · 1 comment · 2 assignees · Opened Mar 18, 2025
add into main pipeline Open

enhancement

nf-core/clipseq#125 · 1 comment · 1 assignee · Opened Mar 18, 2025
adding nf-test to CI workflow Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

nf-core/clipseq#124 · Opened Mar 18, 2025
nf-test Open

enhancement

nf-core/clipseq#123 · 1 assignee · Opened Mar 18, 2025
comment in bindingsitefinder.R script Open

enhancement

nf-core/clipseq#122 · 1 assignee · Opened Mar 18, 2025
Reformat module main.nf to nf-core style Open

enhancement

nf-core/clipseq#121 · 1 assignee · Opened Mar 18, 2025
Add BindingSiteFinder to pipeline Open

enhancement

nf-core/clipseq#120 · 1 comment · 1 assignee · Opened Mar 18, 2025
Address complicated annotation generation Open

enhancement

nf-core/clipseq#119 · 3 assignees · Opened Mar 4, 2025
Make bowtie pre-mapping optional Open

enhancement

nf-core/clipseq#116 · 1 comment · 2 assignees · Opened Jan 28, 2025
BAM entry point Open

enhancement

nf-core/clipseq#112 · 1 comment · 1 assignee · Opened Apr 3, 2024
alternative motifs to peka (homer,streme) Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/clipseq#99 · 1 comment · Opened Jul 12, 2023
option to run icount metagene on peaks Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/clipseq#98 · Opened Jul 12, 2023
demultiplexing Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/clipseq#95 · 1 comment · Opened Jul 12, 2023
add clipqc and multiqc to 2.0 Open

enhancement

nf-core/clipseq#92 · 1 comment · 1 assignee · Opened Jul 6, 2023
documentation for 2.0 Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 10/100

nf-core/clipseq#91 · Opened Jul 6, 2023
making small RNA mapping optional: requires making optional in prepare genome subworkflow and rna align subworkflow Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/clipseq#80 · Opened Jun 21, 2023
adding small RNA default files for supported genomes a la v1.0 Open

nf-core/clipseq#79 · 2 assignees · Opened Jun 21, 2023
MODULE: pureclip Open

Difficulty 5/5 Over a week Newbie friendliness 10/100

nf-core/clipseq#78 · 1 comment · Opened Jun 21, 2023
Conda env fails to create Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/clipseq#71 · Opened Apr 10, 2023
Process `get_software_versions` terminated with an error exit status （1） Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/clipseq#67 · Opened Nov 26, 2022
Reads with / characters in the read names cause the pipeline to fail Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/clipseq#57 · 1 comment · Opened Oct 1, 2021
Add figures to output docs Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 30/100

nf-core/clipseq#49 · Opened Apr 27, 2021

nf-core/clipseq

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