Ekaterina Sakharova

Error in DIAMOND execution

2

Hello, I bumbed into problem with Diamond ``` INFO: Running CheckM2 version 1.0.1 INFO: Custom database path provided for predict run. Checking database at uniref100.KO.1.dmnd... INFO: Running quality prediction workflow...

Hi! I met am issue when tested running several subworkflows in CWLEXEC. My pipeline works fine in CWL (cwltool) but fails in CWLEXEC. The structure of pipeline is very simple:...

Update envs

2

1) Package libtiff conflicts for: ( - libtiff=4.1.0 ) antismash=4.2.0 -> perl-bioperl -> perl-bioperl-core -> perl-gd -> libgd[version='>=2.2.5,=1.0.0,=2.7,=3.2.1,=3.2.1,=3.3,

example5 doesn't work

7

Hi, I've cloned repo and launched example5 `run.sh`. It returned me error ``` ERROR ~ Error executing process > 'foo' Caused by: Process `foo` terminated with an error exit status...

Restructured pipeline to nf-core view - created main.nf main entry - added virify.nf to workflows and simplified - all subworkflows wrapped into separate files - modules moved to local/name/main.nf -...

fixes: - gff lineage - assign taxonomy - krona and sankey plots - updated checkV

Toil doesn't support list of formats in CWL

6

Hello, I have a wf of 2 steps: First step does unzip file. File could be fastA or fastQ. I set it as _[ edam:format_1929, edam:format_1930 ]_ and return file...

Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI). https://bioconda.github.io/recipes/ena-webin-cli/README.html Docs: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html Using in seqsubmit pipeline