Comments (10)
github-actions
commented on July 17, 2024
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days
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molikd
commented on July 17, 2024
This is in progress, and currently running on Ceres
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github-actions
commented on July 17, 2024
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days
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github-actions
commented on July 17, 2024
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days
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Astahlke
commented on July 17, 2024
Will check this
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molikd
commented on July 17, 2024
This and the ag100 documentation issues are the last hurdles for starting to get ag100 people trained on otb
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molikd
commented on July 17, 2024
for reference this genome is in /project/ag100pest/Prosapia_bivincta_otb_test/otb
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github-actions
commented on July 17, 2024
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days
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molikd
commented on July 17, 2024
Currently re-running otb.
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github-actions
commented on July 17, 2024
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days
from otb.
Related Issues (20)
- Bring in gfastats --seq-report? HOT 5
- add -l to the params
- otb.sh needs to be updated for hic/mat/pat reads HOT 1
- gfa2fasta error in phasing mode
- ragtag on haplotypes for scaffolding should be optional. HOT 2
- contributions wiki page and README HOT 2
- process K_mer_counting filt_fastq_ch needs to be flattened so that all input hifi reads are k-mer counted. HOT 1
- env_check needs to check NXF_SINGULARITY_LIBRARYDIR, added to slurm scritps and tutorials HOT 2
- ragtag patch step is hella slow. HOT 4
- generate the hic files HOT 7
- procedures for major tool changes and versioning for otb genomes HOT 1
- otb.sh doesn't handle wildcards handover to nextflow
- FCS-adaptor process add HOT 1
- juicer pre needs to be run again
- Multiple BAM inputs cause bad link to data
- Singularity library cache environmental variables not propagating to scripts
- Possible issue with $BUSCO check in template.slurm files HOT 1
- HiC forward/reverse read files swapped in run.nf HiFiASM call HOT 1
- Pipeline not starting scaffolding steps due to missing --scaffold flag HOT 1
- yahs not finding inter-contig links due to missorted aln.bam file HOT 1
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