cgat-developers cgat-flow issues

cgat-developers / cgat-flow

cgat-flow repository

MIT License

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Regex in pipeline_genesets.py

#161 IanSudbery opened 3 months ago
0
Regex in buildExonTranscript (pipeline_genesets)

#160 jaime11 opened 3 months ago
0
Js current

#159 jscaber closed 2 years ago
2
Fix buildJunctions in mapping pipeline

#158 IanSudbery closed 2 years ago
0
buildJunctions in mapping pipeline produces invalid file

#157 IanSudbery opened 2 years ago
1
bwa_mem2

#156 jscaber closed 2 years ago
0
Missing dependency: mysqlclient

#155 IanSudbery closed 2 years ago
2
Improvements to splicing, bamstats and rnaseq

#154 jscaber closed 2 years ago
0
remove pysam pin

#153 Acribbs closed 2 years ago
3
pysam error

#152 jscaber closed 2 years ago
3
added tmp locations for genesets

#151 Acribbs closed 2 years ago
0
Cutadapt 3.4 no longer accepts --format.

#150 IanSudbery closed 2 years ago
1
Alternate pipeline paths and checksums

#149 IanSudbery opened 2 years ago
2
{is} rnaseqqc repairs

#148 IanSudbery closed 2 years ago
3
No rjson package

#147 IanSudbery closed 2 years ago
0
rnaseqqc - Error setting xlim in plotStrandednessSalmon

#146 IanSudbery opened 2 years ago
9
rnaseqqc - subsetRange produces invalid fastq files

#145 IanSudbery closed 2 years ago
0
Call to fasta2table in RNAseqQC seperates segments with `;`

#144 IanSudbery closed 2 years ago
3
cgat-flow-pipelines.yml causes installation of cgat-apps 0.6.0

#143 IanSudbery opened 2 years ago
12
Ac refactor

#142 Acribbs closed 2 years ago
0
removed references to ruGO and Go.py

#141 Acribbs closed 2 years ago
0
remved mamba 3.8 tests as its broken, will ad back once fixed and add…

#140 Acribbs closed 3 years ago
0
added cython to the conda yml

#139 Acribbs closed 3 years ago
3
RNASeqQC minor bugfix

#138 jscaber closed 3 years ago
0
added github actions tests

#137 Acribbs closed 3 years ago
0
pipeline_genesets assumes that a genome has a miRBase entry

#136 IanSudbery opened 3 years ago
1
{is}bowtie threads

#135 IanSudbery closed 3 years ago
0
installed cutadapt version incompatible with pipeline_readqc

#134 IanSudbery closed 2 years ago
0
Installation breaks cgat-apps bamtools

#133 IanSudbery opened 3 years ago
4
MACS2 is now compatible with python3

#132 IanSudbery opened 3 years ago
1
Js rnaseqdiffexpression.py

#131 Acribbs closed 3 years ago
17
bamstats counts unaligned reads as intergenic.

#130 IanSudbery opened 3 years ago
1
macs2 now a python 3 compatible

#129 Acribbs closed 3 years ago
0
Pin pysam to 0.15.2

#128 sebastian-luna-valero closed 4 years ago
0
install-level script conflicts

#127 Acribbs opened 4 years ago
1
Update install.sh

#126 sebastian-luna-valero closed 4 years ago
4
missing database name in pipeline.yml

#125 Acribbs closed 4 years ago
0
Updated samtools doesn't work with hisat2 in mapping pipeline

#124 microbialman opened 4 years ago
1
SEQUENCEFILES_REGEX in pipeline_rnaseqdiffexpression

#123 IanSudbery closed 4 years ago
3
added sort for capital lettering for certain bigwig files. Should now…

#122 Acribbs closed 4 years ago
0
R functionality in cgatflow

#121 jscaber closed 3 years ago
3
R functionality in cgat

#120 jscaber closed 4 years ago
1
Refactor install-devel.sh

#119 sebastian-luna-valero closed 4 years ago
0
added build_report task as it was missing from readqc pipeline

#118 Acribbs closed 4 years ago
0
Update install-devel.sh to fix Jenkins issue

#117 sebastian-luna-valero closed 4 years ago
0
Testing

#116 Acribbs closed 4 years ago
4
Js rnaseqqc

#115 Acribbs closed 4 years ago
44
Fixes for Bamstats

#114 jscaber closed 4 years ago
6
Conda Env for indexForSailfish error (libboost)

#113 jscaber closed 4 years ago
10
RNASeqQC: transcript FASTA (ensembl98)

#112 jscaber closed 3 years ago
4