ebi-metagenomics-cwl

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Readme how to find data is in https://github.com/BioContainers/containers/tree/master/interproscan/5.30-69.0

mr-c

And point to https://github.com/EBI-Metagenomics/pipeline-v5 more explicitly?

mr-c

containers

4

- [ ] seqprep - [ ] trimmomatic - [ ] evaluate https://github.com/common-workflow-language/workflows/blob/master/tools/trimmomatic-Dockerfile - [ ] "biopython" - [ ] hmmer - [ ] evaluate https://hub.docker.com/r/comics/hmmer/~/dockerfile/ - [ ] FragGeneScan...

mr-c

Rfam library files

1

Hello, First of all - thank you, @mr-c, for the response to my previous problem! I've been further trying to run emg workflows, specifically emg-pipeline-v4-paired.cwl, on my machine. I have...

aperz

toil with CWL on LSF status

4

- [x] ~~Must keep `--workdir` on a non shared filesystem like `/tmp` until https://github.com/BD2KGenomics/toil/pull/1573 is merged (Might be better from a performance perspective anyway)~~ - [x] ~~Make sure to specify...

mr-c

ONT Pipeline

1

We need to start thinking about how we should run ONT data - [x] QC using poretools - [x] Functional assignments using nhmmer and pfam - [ ] The functional...

rdfinn

Need to pull back scaffolds, but we should work on the contigs. A minor tweak in the V4 assembly pipeline. This will make it possible to swap between assemblers.

rdfinn

Add simple binning to the assembly pipeline: - [ ] Install bbmap tool - [ ] Install MetaBat - [ ] See if we can get QC files from metaspades...

rdfinn

Comment about samtools in docker file

1

ebi-metagenomics-cwl/tools/infernal-Dockerfile Is that comment obsolete in this docker file? I think this is just install infernal. Also, we need to have a specific version. Is that version correct?

rdfinn

- [ ] chunking of outputs - [ ] scatter & chunking for other steps, perhaps - [ ] running on OpenLava - [ ] replication at another site -...

mr-c