Comments (3)
Remember to update mermaid diagram on otb landing page before completing.
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initial testing can now proceed, 3f1c137 has required code updates
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testing complete
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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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