cgat-developers/cgat-flow

Issues

• bwa_mem2

  #156 opened 2 years ago by jscaber
  0

• buildJunctions in mapping pipeline produces invalid file

  #157 opened 2 years ago by IanSudbery
  1

• bamstats counts unaligned reads as intergenic.

  #130 opened 4 years ago by IanSudbery
  1

• pipeline_genesets assumes that a genome has a miRBase entry

  #136 opened 4 years ago by IanSudbery
  1

• Duplication of code between bamstats.py and mappingqc.py

  #60 opened 6 years ago by jscaber
  2

• Missing dependency: mysqlclient

  #155 opened 3 years ago by IanSudbery
  2

• cgat-flow-pipelines.yml causes installation of cgat-apps 0.6.0

  #143 opened 3 years ago by IanSudbery
  12

• Installation breaks cgat-apps bamtools

  #133 opened 4 years ago by IanSudbery
  4

• installed cutadapt version incompatible with pipeline_readqc

  #134 opened 3 years ago by IanSudbery
  0

• pysam error

  #152 opened 3 years ago by jscaber
  3

• Call to fasta2table in RNAseqQC seperates segments with `;`

  #144 opened 3 years ago by IanSudbery
  3

• rnaseqqc - subsetRange produces invalid fastq files

  #145 opened 3 years ago by IanSudbery
  0

• rnaseqqc - Error setting xlim in plotStrandednessSalmon

  #146 opened 3 years ago by IanSudbery
  9

• No rjson package

  #147 opened 3 years ago by IanSudbery
  0

• Alternate pipeline paths and checksums

  #149 opened 3 years ago by IanSudbery
  2

• R functionality in cgatflow

  #121 opened 4 years ago by jscaber
  3

• RNASeqQC: transcript FASTA (ensembl98)

  #112 opened 4 years ago by jscaber
  4

• MACS2 is now compatible with python3

  #132 opened 4 years ago by IanSudbery
  1

• install-level script conflicts

  #127 opened 5 years ago by Acribbs
  1

• Conda Env for indexForSailfish error (libboost)

  #113 opened 5 years ago by jscaber
  10

• Updated samtools doesn't work with hisat2 in mapping pipeline

  #124 opened 5 years ago by microbialman
  1

• rpy2 exception rnaseqqc

  #109 opened 5 years ago by jscaber
  4

• GREAT regions

  #103 opened 5 years ago by IanSudbery
  4

• Filter HOT regions

  #102 opened 5 years ago by Acribbs
  0

• STAR read from named pipe

  #79 opened 5 years ago by IanSudbery
  0

• CGATReport parameterization for cgat-flow pipelines

  #42 opened 5 years ago by IanSudbery
  7

• Mapping pipeline does not work with latest version of Bowtie2

  #98 opened 5 years ago by stewalsh04
  5

• Memory in peakcalling checkBams

  #78 opened 6 years ago by IanSudbery
  8

• display of options doesn't work if correct bamfiles are not present

  #44 opened 6 years ago by Charlie-George
  4

• testing: TypeError: zip argument #1 must support iteration

  #91 opened 6 years ago by Acribbs
  5

• Travis tests failing

  #88 opened 6 years ago by Acribbs
  13

• multiple P.run() in one function failing

  #90 opened 6 years ago by Acribbs
  2

• Mapping rate no longer reported by any pipeline

  #85 opened 6 years ago by IanSudbery
  6

• documentation does not refer to use of yml files

  #46 opened 6 years ago by Charlie-George
  4

• Problem with installation enviroment and importing BamTools module - missing compiler?

  #81 opened 6 years ago by stewalsh04
  3

• pipeline_readqc error in pandas concat

  #87 opened 6 years ago by nickilott
  11

• error message during installation of CGAT-core

  #86 opened 6 years ago by amayer21
  5

• Remove instances where ';' is used to join statements

  #52 opened 6 years ago by AndreasHeger
  1

• `bam2bam` usage in pipeline_bamstats

  #76 opened 6 years ago by IanSudbery
  1

• pipeline_readqc.py fails for `ValueError: table is empty` with FastQC tables

  #68 opened 6 years ago by kevinrue
  10

• Pipelines not detecting termination of jobs

  #74 opened 6 years ago by IanSudbery
  7

• Regex for paired sequencing in pipeline_readqc

  #75 opened 6 years ago by IanSudbery
  0

• separate pipelines from tasks

  #51 opened 6 years ago by AndreasHeger
  1

• Segmentation fault error with cluster

  #47 opened 6 years ago by Charlie-George
  12

• Quasimapper Merging Bug - ATTENTION

  #62 opened 6 years ago by jscaber
  7

• Strandedness is the wrong way around in bamstats

  #58 opened 6 years ago by jscaber
  5

• Picard Memory

  #53 opened 6 years ago by jscaber
  2

• single cell qc

  #56 opened 6 years ago by Acribbs
  6

• Command sent to cluster only partially executed [rnaseqqc]

  #57 opened 6 years ago by jscaber
  10

• No transcript_info table with pipeline_genesets

  #50 opened 6 years ago by TomSmithCGAT
  4