elsasserlab/minute

Issues

• bowtie2 2.5.2 crashes when skipping some reads due to read length

  #176 opened 4 months ago by cnluzon
  3

• Optimize minute environment setup

  #190 opened 6 months ago by cnluzon
  3

• Rename percentage duplication field

  #187 opened 9 months ago by cnluzon
  0

• pytz dependency not met in recent builds of conda environment

  #178 opened 10 months ago by cnluzon
  4

• Adjust INRC barplots size for large runs

  #177 opened a year ago by cnluzon
  0

• Read the docs site for minute

  #172 opened a year ago by cnluzon
  1

• Trimming adaptor sequences counts

  #83 opened 4 years ago by cnluzon
  3

• Library size estimation not showing up in stats

  #76 opened a year ago by cnluzon
  2

• Running on SLURM does not delete all temp files

  #100 opened a year ago by cnluzon
  1

• Store intermediate files on $TMPDIR (/scratch)

  #71 opened a year ago by marcelm
  3

• snakemake >= 7.18.2 crashes renaming anonymous rules in some cases

  #159 opened 2 years ago by cnluzon
  3

• Make minute generate bowtie2 index if no index is found

  #162 opened 2 years ago by cnluzon
  0

• Fragment length parameter not so necessary for bigWig generation

  #161 opened 2 years ago by cnluzon
  0

• Add number of demultiplexed reads to stats summary

  #145 opened 2 years ago by cnluzon
  1

• command line cheat sheet

  #157 opened 2 years ago by simonelsasser
  2

• BAM file remove unmapped reads

  #156 opened 2 years ago by simonelsasser
  0

• wrapped snakemake run on cluster mode inherits max ncores from scheduler process

  #155 opened 3 years ago by cnluzon
  0

• Spaces in group name in groups.tsv break the run

  #153 opened 3 years ago by cnluzon
  2

• Rename config.yaml to minute.yaml

  #147 opened 3 years ago by marcelm
  0

• Generated scaling stats missing from the MultiQC report

  #146 opened 3 years ago by cnluzon
  3

• Do we need idxstats?

  #84 opened 3 years ago by marcelm
  1

• Include read demultiplexing barcode in the demultiplexed FASTQ read ID

  #141 opened 3 years ago by cnluzon
  1

• For which libraries should output be generated?

  #93 opened 3 years ago by marcelm
  2

• Should unscaled bigWig files also be generated with --extendReads

  #112 opened 3 years ago by cnluzon
  0

• maplibs does not include all implicit replicate dependencies with pooled in groups.tsv

  #137 opened 3 years ago by cnluzon
  6

• Generate pooled BAM files from their corresponding final clean replicates

  #136 opened 3 years ago by cnluzon
  0

• Warning when a library in libraries.tsv is not present in groups.tsv

  #111 opened 3 years ago by cnluzon
  0

• Make tsv parsing robust to blank spaces

  #134 opened 3 years ago by cnluzon
  3

• Make exclude regions optional

  #103 opened 3 years ago by cnluzon
  0

• Config value for barcode mismatch threshold in demultiplexing rules

  #129 opened 3 years ago by cnluzon
  0

• Add copy number analysis for input

  #124 opened 3 years ago by simonelsasser
  2

• optional fa file

  #104 opened 3 years ago by simonelsasser
  2

• Rule remove_contamination still called with demultiplexed files

  #113 opened 3 years ago by cnluzon
  1

• Should FastQC be ran on demultiplexed libraries?

  #123 opened 3 years ago by cnluzon
  0

• tbb most recent version breaks bowtie2 in conda environment

  #121 opened 3 years ago by cnluzon
  4

• snakemake -n (dry run) does not work anymore

  #115 opened 3 years ago by marcelm
  0

• Pooled bw not generated

  #79 opened 3 years ago by simonelsasser
  3

• Trim/mask read2 sequencing poly-G artifacts

  #107 opened 3 years ago by cnluzon
  4

• warnings/errors: [E::idx_find_and_load] Could not retrieve index file for ...

  #119 opened 3 years ago by marcelm
  1

• Run the pipeline on our GEO submitted data

  #105 opened 3 years ago by cnluzon
  8

• stats_summary.txt has duplicated input lines

  #97 opened 3 years ago by cnluzon
  0

• option to regenerate bw files with custom parameters

  #106 opened 4 years ago by simonelsasser
  0

• Mark duplicates sometimes overflows memory

  #98 opened 4 years ago by cnluzon
  4

• Can the pipeline run as a single cluster job?

  #80 opened 4 years ago by marcelm
  13

• BigWig computation rules are slow

  #89 opened 4 years ago by marcelm
  2

• Group jobs have non-identificative names

  #96 opened 4 years ago by cnluzon
  0

• For reproducibility, Bowtie2 --reorder should be used

  #90 opened 4 years ago by marcelm
  1

• Run low-resource rules local (SLURM)

  #73 opened 4 years ago by cnluzon
  0

• Make demultiplexing faster

  #70 opened 4 years ago by cnluzon
  9

• Move demultiplexed fastq files out of tmp directory

  #74 opened 4 years ago by cnluzon
  0