Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
v2.0.1-g3040c27
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-transcriptomes --bam bams --ref_annotation --ref_genome -profile singularity
Workflow Execution - CLI Execution Profile
None
What happened?
The current workflow does not seem to run pychopper anymore. However the minimap2 alignment parameter kept -uf for both cDNA and dRNA options. This results in wrong strand assignments when applied to cDNAseq data.
Relevant log output
Application activity log entry
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
v2.0.1-g3040c27
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-transcriptomes --bam bams --ref_annotation --ref_genome -profile singularity
Workflow Execution - CLI Execution Profile
None
What happened?
The current workflow does not seem to run pychopper anymore. However the minimap2 alignment parameter kept -uf for both cDNA and dRNA options. This results in wrong strand assignments when applied to cDNAseq data.
Relevant log output
Application activity log entry
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information