open2c/distiller-nf

Issues

• Singularity no space left in tmp directory

  #189 opened 3 months ago by SR-Epi-lab
  0

• Skip deduplication for libraries with UMI

  #188 opened 7 months ago by ChristopherBarrington
  0

• Help with "Error executing process > 'map_parse_sort_chunks...'

  #186 opened 2 years ago by jmteix
  4

• which reference should I cite?

  #185 opened 2 years ago by jane373
  1

• Support of minimap2, bam mem2 and bwa aln

  #181 opened 2 years ago by agalitsyna
  1

• filter with non-int columns

  #184 opened 2 years ago by Phlya
  0

• distiller 0.3.5 roadmap

  #182 opened 2 years ago by agalitsyna
  1

• fastp missing from docker image?

  #159 opened 2 years ago by ChristopherBarrington
  5

• update example cluster config - to match current distiller

  #179 opened 2 years ago by sergpolly
  1

• bam files recycling

  #178 opened 2 years ago by agalitsyna
  0

• library (group) names can't be numerical

  #176 opened 2 years ago by Phlya
  0

• how memory limit gets specified in cluster using

  #175 opened 2 years ago by ryao-mdanderson
  0

• Optional direct fastq downloads from ENA instead of sra-tools

  #174 opened 3 years ago by nvictus
  0

• Iterative mapping

  #173 opened 3 years ago by chorzow
  2

• Bug: split: output file suffixes exhausted

  #169 opened 3 years ago by efriman
  0

• fastq-dump fails with "This sra toolkit installation has not been configured." when docker is disabled

  #157 opened 4 years ago by agalitsyna
  1

• distiller-nf run failed at executing process > 'bin_zoom_library_pairs‘

  #167 opened 3 years ago by hzjsxu
  1

• Remove duplicate reads in sam/bam files

  #165 opened 4 years ago by zhang-jiankun
  0

• Error: Process `map_parse_sort_chunks (library:HSPR2 run:lane1 chunk:0)` terminated with an error exit status (140)

  #166 opened 4 years ago by hzjsxu
  4

• Running without duplicates filtering

  #163 opened 4 years ago by magnitov
  11

• where can I get the specific instructions of the software

  #160 opened 4 years ago by rachelzhu123
  0

• process from 4DN?

  #162 opened 4 years ago by gfudenberg
  0

• distiller (bwa mem) cannot handle Hi-C data sequenced with 25bp

  #141 opened 5 years ago by sergpolly
  9

• Error when trying to run on test dataset

  #161 opened 4 years ago by papelypluma
  13

• What the algorithm is used for balancing Hi-C matrix?

  #154 opened 4 years ago by shappiron
  1

• add phasing

  #158 opened 4 years ago by golobor
  0

• unexpected end of file error

  #156 opened 4 years ago by sabrsyed
  5

• Option to use fastq-dump --split-files, instead of pyfilesplit

  #155 opened 4 years ago by mimakaev
  5

• add fastp trimmer to the docker image so users can do trimming if needed

  #153 opened 4 years ago by mimakaev
  0

• why doesn't distiller-nf require a restriction enzyme option?

  #152 opened 4 years ago by shenscore
  2

• sra download seems to be broken now - some of the ftp links lead nowhere

  #145 opened 5 years ago by sergpolly
  11

• merge_zoom_library_group_coolers and merge_stats... restart again when distiller is restarted (without --resume at least).

  #123 opened 6 years ago by mimakaev
  2

• input verification - check if the folder doesn't already have ./work and ./results from tests

  #150 opened 5 years ago by golobor
  0

• [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)

  #149 opened 5 years ago by gopel
  4

• built-in adaptor trimming

  #146 opened 5 years ago by gspracklin
  4

• Input verification - ensure no duplicated input files

  #147 opened 5 years ago by Phlya
  0

• Have an option to use fastq-dump even to download a whole .sra file

  #144 opened 5 years ago by mimakaev
  0

• travis is failing to download the test sample fastq-s

  #135 opened 6 years ago by sergpolly
  2

• having no map options, i.e. empty dict, leads to nextflow error

  #142 opened 5 years ago by sergpolly
  1

• distiller is failing at merge_zoom_library_group_coolers

  #136 opened 6 years ago by nandankita
  8

• distiller is failing at bin_zoom_library_pairs with new reference genome

  #137 opened 6 years ago by gibcus
  9

• why dropreadID is ignored when makePairsam is False

  #133 opened 6 years ago by sergpolly
  7

• raise error if important parameters not provided

  #127 opened 6 years ago by mimakaev
  1

• Check for illegal characters in library names

  #124 opened 6 years ago by mimakaev
  1

• balance\no balance option

  #126 opened 6 years ago by azkalot1
  3

• binning uses config specified decompression command, should use gz-one

  #131 opened 6 years ago by sergpolly
  1

• use cooler cload pairs --tmpdir

  #129 opened 6 years ago by golobor
  0

• Set OpenMP variables to one thread, just in case numpy tries to turn on multithreading

  #128 opened 6 years ago by mimakaev
  0

• By default, delete .cool files and keep only .mcool

  #125 opened 6 years ago by mimakaev
  0

• [Proposal] Genome name in filenames?

  #122 opened 6 years ago by mimakaev
  2