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31 Open 43 Closed
31 Open 43 Closed
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Issues list

Use workflows instead of profiles for different pipelines
#86 opened Jun 25, 2024 by emi80
Redefine processing from input BAM files
#85 opened Jun 21, 2024 by emi80
Update RSEM version
#83 opened May 3, 2024 by emi80
1 task
1
Set credibility intervals computation as optional in RSEM module
#82 opened May 2, 2024 by emi80
Modules refactoring
#81 opened May 2, 2024 by emi80
1 task
STAR mapping
#80 opened Aug 6, 2023 by RamilNurtdinov
Paired end as 'false' in the 'general parameters' log is confusing
#79 opened Aug 1, 2023 by emi80
STAR 2.4.0j with singularity gives segmentation fault error
#67 opened Dec 9, 2022 by asalhab
3
Introduce automated generation of quantification matrix
#65 opened Jan 20, 2022 by marangiop
Include FastQC
#63 opened Jan 20, 2022 by marangiop
sambamba-sort: couldn't parse --memory-limit option
#60 opened Feb 15, 2021 by jpang-van
3
Update readme with a section describing output files
#58 opened Jan 4, 2021 by emi80
1
grape-nf does not execute some steps
#57 opened Oct 16, 2020 by asalhab
2
the link to the provided conda environemnt file is corrupted
#56 opened Oct 12, 2020 by asalhab
1
Markdup step TimeOut exiting with IHEC usage
#53 opened Nov 11, 2019 by paulstretenowich
13
Bamstats process fails with unsorted annotation
#52 opened Oct 9, 2019 by emi80
Check input bam files for library type
#49 opened Sep 30, 2019 by emi80
Sambamba cannot merge transcriptome bams as they are unsorted
#48 opened Sep 30, 2019 by emi80
Expose tool options to Nextflow config file
#37 opened Jul 25, 2018 by emi80
Add MultiQC step
#36 opened Jun 20, 2018 by emi80
Add pseudo-alignment based quantification tools
#35 opened Jun 20, 2018 by emi80
Use maps instead of sets for storing samples metadata
#34 opened Jun 20, 2018 by emi80
Use publishDir to store pipeline results
#33 opened Jun 20, 2018 by emi80
STAR alignment for multiple lane fastq
#31 opened May 28, 2018 by Pitithat-pu
1
Switch to nf-test for testing modules and workflows
#30 opened Apr 6, 2018 by emi80
ProTip! no:milestone will show everything without a milestone.