jjfarrell

Hi @ctsa Lots of academic institutions using SGE have or are planning to migrate to SLURM. This is lately driven since SGE is now no longer supported. Is there any...

I just started using 4.3 and see that there are new contigs but they are missing the chr for some reason. The contigs are out of order also. So in...

I took a quick look at the code. It looks like the withChr = True is based on the input vcf. Since the impute aligned to 37 has no chr,...

So this became a problem when the GRCh37 was not consistent with GRCh38 using chr. Would using the target reference to test for withCHR instead of the input VCF fix...

@clairemerot @jbelyeu Since it plots DELs great, maybe this is an approach to visualize INS. Essentially turn the INS into a Deletion with a new reference containing the INS sequence....

Placing the names to the left of the corresponding isoform with the names right-justified against each isoform figure I think would work.

Could a cram be streamed with samtools to KMC standard input as a short term workaround? This would help minimize the storage requirements and increase the throughput.

To test the changes, I modified tests/publish-dir.nf to add a sleep 1m between the creation of the bam and bai. ``` #!/usr/bin/env nextflow process align { publishDir 'data', mode: 'copy'...

@srynobio @pditommaso @lindenb Several bioinformatics tools output both the vcf.gz and vcf.gz.tbi files. As described above, the present publishDir copy mode often results with files that have the vcf.gz.tbi that...

@pditommaso Multiple posters are waiting for a resolution to this issue.   Why not simply preserve the time stamp of the working directory files when copying published  files? This avoids breaking...