Closed pratarora closed 6 months ago
Ubuntu 22.04
No response
Nextflow version version 23.10.1, build 5891
Command line
wf-single-cell v1.0.3-g890cab0
nextflow run epi2me-labs/wf-single-cell --fastq /mnt/disk2/Carla_seq/LRONT_samples/CI_1/CI_1.pass.fastq.gz --sample CI_1 --out_dir nextflow_results_CI_1_test --kit_name 3prime --kit_version v3 --ref_genome_dir /mnt/disk2/Carla_seq/reference_genomes/Ensembl/Danio_rerio/GRCz11/v111/v111_10X/ --merge_bam True --matrix_max_mito 60 -profile standard --max_threads 20 --resources_mm2_max_threads 20 --resources_mm2_flags '-I 48G' --mito_prefix mt-
standard (default)
we had an issue where stringtie was failing. (https://github.com/epi2me-labs/wf-single-cell/issues/83). We dug more into this problem and contacted the authors of stringtie. they have released a new version which has possibly resolved this problem. Could you kindly update/provide the dockerfile so that we can remake the docker with the latest version of stringtie v2.2? (https://github.com/gpertea/stringtie/issues/320) (https://github.com/gpertea/stringtie/releases/tag/v2.2.2) Looking forward to your reply!
no logs
yes
Duplicate #83
cjw85
commented
6 months ago cjw85
commented
6 months ago
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
Nextflow version version 23.10.1, build 5891
Workflow Execution
Command line
EPI2ME Version
wf-single-cell v1.0.3-g890cab0
CLI command run
nextflow run epi2me-labs/wf-single-cell --fastq /mnt/disk2/Carla_seq/LRONT_samples/CI_1/CI_1.pass.fastq.gz --sample CI_1 --out_dir nextflow_results_CI_1_test --kit_name 3prime --kit_version v3 --ref_genome_dir /mnt/disk2/Carla_seq/reference_genomes/Ensembl/Danio_rerio/GRCz11/v111/v111_10X/ --merge_bam True --matrix_max_mito 60 -profile standard --max_threads 20 --resources_mm2_max_threads 20 --resources_mm2_flags '-I 48G' --mito_prefix mt-
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
we had an issue where stringtie was failing. (https://github.com/epi2me-labs/wf-single-cell/issues/83). We dug more into this problem and contacted the authors of stringtie. they have released a new version which has possibly resolved this problem. Could you kindly update/provide the dockerfile so that we can remake the docker with the latest version of stringtie v2.2? (https://github.com/gpertea/stringtie/issues/320) (https://github.com/gpertea/stringtie/releases/tag/v2.2.2) Looking forward to your reply!
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response