guigolab grape-nf issues

guigolab / grape-nf

An automated RNA-seq pipeline using Nextflow

GNU General Public License v3.0

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issues

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Use workflows instead of profiles for different pipelines

#86 emi80 opened 4 months ago
0
Redefine processing from input BAM files

#85 emi80 opened 5 months ago
0
Error when passing annotation as a relative path to QC subworkflow

#84 vntasis closed 5 months ago
0
Update RSEM version

#83 emi80 opened 6 months ago
1
Set credibility intervals computation as optional in RSEM module

#82 emi80 opened 6 months ago
0
Modules refactoring

#81 emi80 opened 6 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 2 years 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 7 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 4 years ago
2
the link to the provided conda environemnt file is corrupted

#56 asalhab opened 4 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 5 years ago
13
Bamstats process fails with unsorted annotation

#52 emi80 opened 5 years ago
0
Pipeline refactoring

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

#50 emi80 closed 7 months ago
1
Check input bam files for library type

#49 emi80 opened 5 years ago
0
Sambamba cannot merge transcriptome bams as they are unsorted

#48 emi80 opened 5 years ago
0
Move inferExp after markdup step

#47 emi80 closed 7 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 6 years ago
0
Use sambamba in most pipeline processes

#41 emi80 closed 6 years ago
0
Add mark-duplicates step

#40 emi80 closed 6 years ago
0
Update configuration files to use process selectors

#39 emi80 closed 6 years ago
0
Citation information

#38 karl616 closed 7 months ago
4
Expose tool options to Nextflow config file

#37 emi80 opened 6 years ago
0