nf-core/hic

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Analysis of Chromosome Conformation Capture data (Hi-C)

Stars: 112
Forks: 68
Open beginner issues: 0
Indexed issues: 43

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 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

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43 open issues indexed

Issue in test run with conda Open

bug

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

nf-core/hic#239 · Opened Mar 13, 2026
The nf-core/hic pipeline is still running, but no further results have been generated after contact_maps/bins Open

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

nf-core/hic#235 · Opened Feb 12, 2026
ERROR ~ * --res_zoomify: expected type: String, found: Integer (5000) Open

bug

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

nf-core/hic#229 · 1 reaction · Opened Jun 24, 2025
MATPLOTLIB warning derails parsing cooltools version in collated_versions.yml during NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nf-core/hic#227 · Opened Jun 12, 2025
Improve pipeline for Arima Hi-C protocol Open

bug

nf-core/hic#225 · 1 comment · 1 assignee · Opened Jun 3, 2025
get_restriction_fragments tag fails on AWS Open

nf-core/hic#224 · 1 assignee · Opened May 15, 2025
Merging replicates for analysis Open

enhancement

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

nf-core/hic#223 · Opened May 7, 2025
MultiQC does not report all samples Open

bug

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

nf-core/hic#221 · Opened Apr 29, 2025
Compress .allValidPairs and .txt files Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/hic#220 · Opened Apr 28, 2025
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})' Open

bug

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

nf-core/hic#218 · 2 comments · Opened Apr 9, 2025
JSON schema: Hic Open

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

nf-core/hic#217 · Opened Mar 25, 2025
Bin size parameter not read Open

bug

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

nf-core/hic#216 · Opened Mar 11, 2025
GET_RESTRICTION_FRAGMENTS cannot read compressed genome file Open

bug

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

nf-core/hic#215 · Opened Feb 14, 2025
TRIM_READS error Open

bug

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

nf-core/hic#210 · Opened Nov 21, 2024
Cannot edit config files Open

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

nf-core/hic#209 · 2 comments · Opened Nov 1, 2024
bug with the bowtie2 2.5.2 Open

bug

nf-core/hic#208 · 1 comment · 1 assignee · Opened Oct 22, 2024
Reopening the split-fastq error Open

bug

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

nf-core/hic#198 · 1 comment · Opened Apr 30, 2024
Improve multiQC report Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nf-core/hic#190 · Opened Jan 26, 2024
Add loop calling tools Open

enhancement

nf-core/hic#189 · 2 comments · 1 assignee · Opened Jan 26, 2024
add calder2 module Open

enhancement

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

nf-core/hic#188 · Opened Jan 26, 2024
sort extreme large pairs files Open

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

nf-core/hic#176 · 1 reaction · Opened Aug 3, 2023
Put FastQ File Splitting in a Dedicated Process Open

enhancement

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

nf-core/hic#164 · 9 comments · 1 reaction · Opened May 17, 2023
Include pairtools protocol Open

enhancement

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

nf-core/hic#162 · 7 comments · Opened May 5, 2023
Change bwt2_index input to take input tar/tar.gz file rather than path + base name Open

enhancement

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

nf-core/hic#157 · Opened Apr 4, 2023
samplesheet check too stringent for header check Open

bug

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

nf-core/hic#152 · 8 comments · Opened Mar 7, 2023
Chromap Open

enhancement

nf-core/hic#134 · 1 assignee · Opened Aug 14, 2022
update cooltools compartments Open

enhancement

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

nf-core/hic#133 · 1 comment · Opened Jul 29, 2022
bowtie2 indexes lost for genomes bigger than 4Gbp when --bwt2_index is not provided Open

bug

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

nf-core/hic#131 · 3 comments · Opened Jul 18, 2022
singularity fails to pull the hic-1.3.0 container Open

bug

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

nf-core/hic#129 · Opened Jun 23, 2022
Pipeline failure on second read during bowtie2_end_to_end Open

bug

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

nf-core/hic#128 · Opened Jun 17, 2022
Buffer underflow on -resume Open

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

nf-core/hic#121 · Opened Mar 18, 2022
perserve the qc pdf from hic pro Open

enhancement

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

nf-core/hic#118 · Opened Feb 9, 2022
get_valid_interaction fails with exitcode 137 with --digestion arima Open

bug

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

nf-core/hic#113 · 7 comments · Opened Nov 10, 2021
conda environment error Open

bug

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

nf-core/hic#109 · 5 comments · Opened Sep 24, 2021
Input File Naming Convention Open

bug

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

nf-core/hic#92 · 1 comment · Opened Feb 24, 2021
design file Open

enhancement

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

nf-core/hic#63 · Opened Jun 11, 2020
reported bugs Open

bug

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

nf-core/hic#62 · 2 comments · Opened Jun 11, 2020
stepwise mode Open

enhancement

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

nf-core/hic#56 · 1 reaction · Opened May 19, 2020
count vs distance decay curve Open

enhancement

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

nf-core/hic#54 · 1 comment · Opened May 19, 2020
add support for .hic file due to new UCSC tracks format Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/hic#44 · 1 comment · Opened Nov 22, 2019
support for capture Hi-C Open

enhancement

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

nf-core/hic#34 · Opened Oct 9, 2019
installation process Open

question

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

nf-core/hic#16 · 4 comments · Opened Apr 30, 2019
support for allele-specific analysis Open

enhancement

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

nf-core/hic#15 · 2 comments · Opened Apr 30, 2019

nf-core/hic

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