guigolab grape-nf issues

guigolab / grape-nf

An automated RNA-seq pipeline using Nextflow

GNU General Public License v3.0

36 stars 10 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Use workflows instead of profiles for different pipelines

#86 emi80 opened 2 months ago
0
Redefine processing from input BAM files

#85 emi80 opened 2 months ago
0
Error when passing annotation as a relative path to QC subworkflow

#84 vntasis closed 3 months ago
0
Update RSEM version

#83 emi80 opened 4 months ago
1
Set credibility intervals computation as optional in RSEM module

#82 emi80 opened 4 months ago
0
Modules refactoring

#81 emi80 opened 4 months ago
0
STAR mapping

#80 RamilNurtdinov opened 1 year ago
0
Paired end as 'false' in the 'general parameters' log is confusing

#79 emi80 opened 1 year ago
0
DSL2 refactoring improvement

#78 emi80 closed 1 year ago
0
Wrong paired-end information in pipeline db for input bams

#77 emi80 closed 1 year ago
0
Fix failing bigwig and quantification processes when bam file has no mapped reads

#76 emi80 closed 1 year ago
0
add CFF file to the repository to allow citation

#75 proccaserra closed 1 year ago
1
Fix reported number of sequencing runs in log

#74 emi80 closed 1 year ago
0
Include sample id in process tags

#73 emi80 closed 1 year ago
0
Bad quantifications and bamStatsFiles channels when run IDs are not globally uniq

#72 emi80 closed 1 year ago
0
inferExp step fails with mixed protocol BAM file

#71 emi80 closed 1 year ago
1
Wrong memory setting in mapping process

#70 emi80 closed 1 year ago
0
Dsl2

#69 marangiop closed 1 year ago
0
Bump asciidoctor from 1.5.4 to 1.5.8 in /docs

#68 dependabot[bot] closed 1 year ago
0
STAR 2.4.0j with singularity gives segmentation fault error

#67 asalhab opened 1 year ago
3
Memory issue when generating STAR index

#66 emi80 closed 1 year ago
0
Introduce automated generation of quantification matrix

#65 marangiop opened 2 years ago
0
Introduce compatibility for 3' end sequenced datasets

#64 marangiop closed 5 months ago
1
Include FastQC

#63 marangiop opened 2 years ago
0
Migrate to Nextflow DSL 2

#62 marangiop closed 1 year ago
0
Bump addressable from 2.4.0 to 2.8.0 in /docs

#61 dependabot[bot] closed 3 years ago
0
sambamba-sort: couldn't parse --memory-limit option

#60 jpang-van opened 3 years ago
3
Change view for the quantification process

#59 emi80 closed 3 years ago
1
Update readme with a section describing output files

#58 emi80 opened 3 years ago
1
grape-nf does not execute some steps

#57 asalhab opened 3 years ago
2
the link to the provided conda environemnt file is corrupted

#56 asalhab opened 3 years ago
1
Wrong samples/ids stats for merging detection

#55 emi80 closed 4 years ago
0
Add support for GFF annotation

#54 emi80 closed 4 years ago
1
Markdup step TimeOut exiting with IHEC usage

#53 paulstretenowich opened 4 years ago
13
Bamstats process fails with unsorted annotation

#52 emi80 opened 4 years ago
0
Pipeline refactoring

#51 emi80 closed 4 years ago
0
Move bam sorting to a standalone process

#50 emi80 closed 5 months ago
1
Check input bam files for library type

#49 emi80 opened 4 years ago
0
Sambamba cannot merge transcriptome bams as they are unsorted

#48 emi80 opened 4 years ago
0
Move inferExp after markdup step

#47 emi80 closed 5 months ago
1
Replace deprecated groupBy operator

#46 emi80 closed 5 years ago
0
Add support for compressed reference files

#45 emi80 closed 5 years ago
1
Add support for compressed reference files

#44 emi80 closed 5 years ago
0
Add step to download input data

#43 emi80 closed 5 years ago
0
Add step to get mapping statistics

#42 emi80 closed 5 years ago
0
Use sambamba in most pipeline processes

#41 emi80 closed 5 years ago
0
Add mark-duplicates step

#40 emi80 closed 5 years ago
0
Update configuration files to use process selectors

#39 emi80 closed 5 years ago
0
Citation information

#38 karl616 closed 5 months ago
4
Expose tool options to Nextflow config file

#37 emi80 opened 6 years ago
0