open2c / distiller-nf

A modular Hi-C mapping pipeline

open2c/distiller-nf Issues

Skip deduplication for libraries with UMI
Updated 4 months ago
Help with "Error executing process > 'map_parse_sort_chunks...'
Closed a year ago4
which reference should I cite?
Updated 2 years ago1
Support of minimap2, bam mem2 and bwa aln
Updated 2 years ago1
filter with non-int columns
Updated 2 years ago
distiller 0.3.5 roadmap
Updated 2 years ago1
fastp missing from docker image?
Closed 2 years ago5
update example cluster config - to match current distiller
Updated 2 years ago1
bam files recycling
Updated 2 years ago
library (group) names can't be numerical
Updated 2 years ago
how memory limit gets specified in cluster using
Updated 2 years ago
Optional direct fastq downloads from ENA instead of sra-tools
Updated 2 years ago
Iterative mapping
Closed 2 years ago2
Bug: split: output file suffixes exhausted
Updated 3 years ago
fastq-dump fails with "This sra toolkit installation has not been configured." when docker is disabled
Updated 3 years ago1
distiller-nf run failed at executing process > 'bin_zoom_library_pairs‘
Closed 3 years ago1
Remove duplicate reads in sam/bam files
Closed 3 years ago
Error: Process `map_parse_sort_chunks (library:HSPR2 run:lane1 chunk:0)` terminated with an error exit status (140)
Closed 3 years ago4
Running without duplicates filtering
Closed 4 years ago11
where can I get the specific instructions of the software
Closed 4 years ago
process from 4DN?
Updated 4 years ago
distiller (bwa mem) cannot handle Hi-C data sequenced with 25bp
Updated 4 years ago9
Error when trying to run on test dataset
Closed 4 years ago13
What the algorithm is used for balancing Hi-C matrix?
Closed 4 years ago1
add phasing
Updated 4 years ago
unexpected end of file error
Closed 4 years ago5
Option to use fastq-dump --split-files, instead of pyfilesplit
Closed 4 years ago5
add fastp trimmer to the docker image so users can do trimming if needed
Updated 4 years ago
why doesn't distiller-nf require a restriction enzyme option?
Closed 4 years ago2
sra download seems to be broken now - some of the ftp links lead nowhere
Updated 4 years ago11
merge_zoom_library_group_coolers and merge_stats... restart again when distiller is restarted (without --resume at least).
Updated 4 years ago2
input verification - check if the folder doesn't already have ./work and ./results from tests
Updated 4 years ago
[89/ab2821] NOTE: Process `map_parse_sort_chunks (library:your_library_name_1 run:lane1 chunk:0)` terminated with an error exit status (127) -- Execution is retried (1)
Closed 4 years ago4
built-in adaptor trimming
Updated 4 years ago4
Input verification - ensure no duplicated input files
Updated 5 years ago
Have an option to use fastq-dump even to download a whole .sra file
Updated 5 years ago
travis is failing to download the test sample fastq-s
Updated 5 years ago2
having no map options, i.e. empty dict, leads to nextflow error
Updated 5 years ago1
distiller is failing at merge_zoom_library_group_coolers
Closed 5 years ago8
distiller is failing at bin_zoom_library_pairs with new reference genome
Updated 5 years ago9
why dropreadID is ignored when makePairsam is False
Closed 5 years ago7
raise error if important parameters not provided
Updated 5 years ago1
Check for illegal characters in library names
Closed 5 years ago1
balance\no balance option
Closed 5 years ago3
binning uses config specified decompression command, should use gz-one
Closed 5 years ago1
use cooler cload pairs --tmpdir
Updated 5 years ago
Set OpenMP variables to one thread, just in case numpy tries to turn on multithreading
Updated 6 years ago
By default, delete .cool files and keep only .mcool
Updated 6 years ago
let the user choose if the temporary folder is created in /tmp or in the work folder
Closed 6 years ago1
[Proposal] Genome name in filenames?
Closed 6 years ago2