karlestira

Threading randomness issue in fastq files is reproducible, but the output is still randomly in stdout because using fwrite to STDOUT in multi-threading. I am using fastp 0.23.1.

Any way to skip fasta md5 check when generating CRAM file from BAM/SAM?

1

#### Is your feature request related to a problem? Please specify. samtools view / sort will cost a lot of time(~20s on my computer) to read genome file(the fasta), and...

Bowtie2 always fully use CPUs, regardless of input state. For example: bgzip -cd r1.fq.gz | tee >(bowtie2 -x genome.fasta -U /dev/stdin > /dev/null) | less When command less blocks its...

Any way to get command line settings in snakefile

2

Is there any way to know the command line of snakemake? I want to know what profile-file(--profile) my users used, to record some params(for example: singularity-args). That means I want...