Giulio Genovese

Indeed, the following workflow: ``` $ echo 'version development workflow main { input { Directory d = "/etc" } }' > main.wdl ``` Will fail the womtool parser: ``` $...

Thank you for looking into this! I am using what I think is currently the latest version, that is, 51 (i.e. running it with `java -jar cromwell-51.jar run test.wdl -i...

I think the following workflow (test.wdl) shows some even more insidious issues with localization: ``` version 1.0 workflow main { call main { input: X = ["/tmp/1", "/tmp/2", "/tmp/3"], Y...

This problem arose in my organization as they are using Cisco AnyConnect. I find it weird that I can browse the website `https://vpn.######.org/CACHE/sdesktop/hostscan/linux_x64/manifest` with Firefox but I cannot download the...

An even cleaner workaround: `echo -e "openssl_conf = openssl_init\n[openssl_init]\nssl_conf = ssl_sect\n[ssl_sect]\nsystem_default = system_default_sect\n[system_default_sect]\nOptions = UnsafeLegacyRenegotiation" | OPENSSL_CONF=/dev/stdin curl https://old-host/`

I have encountered the same issue in a completely reproducible way. I used the cholmod_gpu_stats() to display how much time was spent in each function. When CHOLMOD 4.0.3 was linked...

@martin-frbg, this is not the same reproducer. Somehow it seems that all of my matrices are affected by this issue. And I had not understood before that CHOLMOD 4 limits...

Unfortunately not. In some WDLs I generate the suffix array with a scatter loop and then I send the string array as an input for a task. It is quite...

I have tried the following on the 1000 Genomes reference panel for chromosome 22 (3,202 samples, 1,066,557 variants): ``` $ time bcftools +fill-tags -Ou 1kGP_high_coverage_Illumina.chr22.bcf -o /dev/null -- -t AN,AC...

These are errors from the [bgzf.c](https://github.com/samtools/htslib/blob/develop/bgzf.c) file so most likely your input files are malformed. Maybe try to re-index them again. What version of BCFtools/HTSlib/MoChA are you using?