CRG-CNAG CalliNGS-NF issues

CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

Mozilla Public License 2.0

130 stars 53 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

ERROR: Input files reference and features have incompatible contigs

#36 kyle-lk opened 1 year ago
0
Operator `phase` is deprecated

#35 HudoGriz opened 1 year ago
0
Few fixes

#34 kstawiski opened 1 year ago
0
Process `ASE_KNOWNSNPS (SAMPLE123XYZ)` terminated with an error exit status (2) (More then one variant context at position: chr3:XXXXXXX)

#33 SINGHVJ-Bio opened 2 years ago
2
Documentation issue?

#32 pieterlukasse opened 2 years ago
2
denylisted genome file

#31 okeyoallan opened 2 years ago
0
Could not build fai index genome.fa.fai

#30 Jokendo-collab opened 2 years ago
0
will there be a nf of dna variant calling which need paired samples

#29 asmlgkj opened 2 years ago
0
Fix build badge in README.md

#28 kojix2 closed 2 years ago
2
Use option instead of genome regeneration in STAR for 2-pass mapping

#27 kojix2 closed 2 years ago
1
The on-the-fly two-pass option could be used to avoid the genome regeneration step

#26 kojix2 closed 2 years ago
3
Testing with GithubActions

#25 kojix2 closed 2 years ago
1
Fix a typo

#24 kojix2 closed 2 years ago
1
mm39 variants / black list

#23 sarahbonnin opened 3 years ago
4
could not execute mkdir

#22 ghost closed 3 years ago
1
Process POST_PROCESS_VCF failes when order of chromosomes in result.DP8.vcf differs from that in the GRCm38/Annotation/Variation/Mus_musculus.vcf

#21 dylanht opened 3 years ago
0
Whether do not generate star index if provide directly?

#20 RyanYip-Kat opened 3 years ago
1
Reading single end reads

#19 Jokendo-collab opened 3 years ago
4
Error: Unable to access jarfile /scratch/oknjav001/transcriptomics/proteogenomics/variabtcalling/gatk/gatk3.7/GenomeAnalysisTK.jar

#18 Jokendo-collab closed 3 years ago
1
Cannot locate GATK.jar file

#17 Jokendo-collab closed 3 years ago
1
suggest adding docker runOptions to nextflow.config

#16 jayoung closed 3 years ago
1
Use GATK4 integrated Picard

#15 jdwheaton closed 3 years ago
2
GATK4 branch does not require separate Picard

#14 jdwheaton closed 3 years ago
3
The genomeDir dir name is confusing

#13 pditommaso closed 3 years ago
0
simplify star 2 pass alignment

#12 alexyfyf closed 3 years ago
1
Using Single end data

#11 benkraj closed 4 years ago
5
picard.jar not found

#10 robertobarrero closed 3 years ago
1
samtools: command not found

#9 cailiangliang765 closed 3 years ago
3
containerOverrides for AWS BATCH

#8 Dharmendra-G-1 opened 5 years ago
1
adapting to GATK4

#7 lucacozzuto closed 5 years ago
2
GATK license

#6 lynnlangit closed 3 years ago
1
Error in SplitNCigarReads step

#5 slagtermaarten closed 5 years ago
3
Implement support for GATK4

#4 pditommaso closed 3 years ago
17
Variant calling step failing when using process scratch

#3 pditommaso closed 6 years ago
1
Typo in the title of the flow-chart picture.

#2 pditommaso closed 7 years ago
0
CalliNGS-NF

#1 evanfloden closed 7 years ago
1