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nf-core
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rnavar
gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
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Pipeline does not run through GATK step
#150
KristinaGagalova
opened
3 months ago
2
ch_fasta_fai and ch_gtf fix after nf-core/tools v2.14.1 merge
#149
nschcolnicov
closed
3 months ago
1
Ungzipped GTF created in PREPARE_GENOME subworkflow not being used
#148
nschcolnicov
closed
3 months ago
1
Thoughts on submitting RNAVar to a journal?
#147
Shaun-Regenbaum
opened
3 months ago
0
Add a bgzip module for dbsnp files
#146
nschcolnicov
opened
3 months ago
0
dev branch works only on the first sample
#145
loipf
opened
3 months ago
4
Change gatk_vf params from integer to floats
#144
robsyme
closed
3 months ago
1
add contig ignore to beintervals
#143
maxulysse
closed
3 months ago
1
Fix dbsnp usage
#142
maxulysse
closed
4 months ago
1
Fix reference files usage
#141
maxulysse
opened
4 months ago
1
Important! Template update for nf-core/tools v2.14.1
#140
nf-core-bot
closed
4 months ago
1
Important! Template update for nf-core/tools v2.14.0
#139
nf-core-bot
closed
4 months ago
1
Adding gvcf
#138
maxulysse
closed
4 months ago
2
Adding gvcf
#137
maxulysse
closed
4 months ago
3
Replaced UNZIP with GUNZIP
#136
nschcolnicov
closed
6 months ago
2
UNZIPPED files are not being properly staged when running on aws
#135
nschcolnicov
closed
6 months ago
1
preprocessing output directory contains more subdirectories than the number of samples processed
#134
nschcolnicov
closed
6 months ago
1
Important! Template update for nf-core/tools v2.13.1
#133
nf-core-bot
closed
4 months ago
1
Fixed null value in publish dir
#132
nschcolnicov
closed
7 months ago
1
Important! Template update for nf-core/tools v2.13
#131
nf-core-bot
closed
7 months ago
0
Added missing defs
#130
nschcolnicov
closed
7 months ago
1
Paired end files are being classified as single_end: true
#129
nschcolnicov
closed
7 months ago
1
NFCORE_RNAVAR:RNAVAR:GATK4_MERGEVCFS fails with error "has sample entries that don't match the other files"
#128
nschcolnicov
closed
7 months ago
2
Fixed VEP s3 bucket path
#127
nschcolnicov
closed
7 months ago
1
VEP cache is not working
#126
nschcolnicov
closed
7 months ago
4
SnpEff and VEP publishDir contains a variable with a null value
#125
nschcolnicov
closed
7 months ago
1
Fixed S3 bucket path in conditional statements
#124
nschcolnicov
closed
7 months ago
2
Test full profile is not working
#123
nschcolnicov
opened
7 months ago
2
Pipeline doesn't build the right path to the vep cache files
#122
nschcolnicov
closed
7 months ago
2
SNPEFF_SNPEEF fails due to not finding snpEffPredictor.bin file
#121
nschcolnicov
closed
7 months ago
2
Important! Template update for nf-core/tools v2.12
#120
nf-core-bot
closed
7 months ago
2
SplitNCigarReads: sample cross-contamination
#119
dbatrakou
opened
8 months ago
0
It is possible to make "known indels" and "dbsnp" databases optional in this pipeline as was done in Sarek?
#118
Jokendo-collab
opened
8 months ago
3
Nf core template merge 2.11.1
#117
maxulysse
closed
9 months ago
2
Added unzip feature
#116
nschcolnicov
closed
8 months ago
6
Add the possibility of usiing gzipped fasta and gtf files
#115
nschcolnicov
closed
7 months ago
2
Adding a filtering step to handle unplaced chromosomal sequences. V2
#114
Shaun-Regenbaum
opened
9 months ago
5
Adding a filtering step to handle unplaced chromosomal sequences.
#113
Shaun-Regenbaum
closed
9 months ago
2
Failure on GATK4_BEDTOINTERVALLIST due to incorrect exome.bed generation from iGenomes References.
#112
Shaun-Regenbaum
opened
9 months ago
5
Important! Template update for nf-core/tools v2.11
#111
nf-core-bot
closed
9 months ago
1
Add samtools mpileup as an alternative variant caller
#110
Leon-Bichmann
opened
10 months ago
0
update all modules
#109
maxulysse
closed
11 months ago
2
input file name collision
#108
vivischuch
opened
11 months ago
5
FIX: issues reported on Slack
#107
maxulysse
closed
11 months ago
1
fix vep_cache
#106
bounlu
closed
7 months ago
2
fix ch_dict
#105
bounlu
closed
11 months ago
1
temporary fix for #103
#104
bounlu
closed
11 months ago
1
`dev` version gets stuck at Launching step
#103
bounlu
opened
11 months ago
0
fix process name SNPEFF_SNPEFF
#102
bounlu
closed
11 months ago
1
fix process name for SNPEFF_SNPEFF
#101
bounlu
closed
11 months ago
1
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