hadge

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souporcell_pipeline.py: command not found

1

Hi again! Sorry if I cause a lot of errors, really appreciate all your help! > Caused by: > Process `HADGE:run_multi:gene_demultiplexing:demultiplex_souporcell:souporcell (sampleID)` terminated with an error exit status (127) >...

bednarsky

improve description of inputs

5

@mari-ga and @wxicu please modify the section on minimum required inputs following this: The hashing and genetic mode are two independent workflows, and the rescue mode allows to perform joint...

bio-la

Souporcell fails due to bcftools not found

2

Hi! I am running the newest version of the pipeline on some more samples and encountered a new error: > ERROR ~ Error executing process > 'HADGE:run_multi:gene_demultiplexing:demultiplex_souporcell:souporcell (sample_name)' > >...

bednarsky

Missing conda recipes

2

- [x] cellhashr - [x] gmmdemux - [ ] Souporcell - [x] Vireo - [x] cellsnp (just cellsnp lite in recipes) - [x] freemuxlet - [x] scsplit

Zethson

freebayes could not parse maxComplexGap

2

Hi again, and thanks again for all the help with the great pipeline! Now this error: > ERROR ~ Error executing process > 'HADGE:run_multi:gene_demultiplexing:variant_freebayes:freebayes (sid456)' > > Caused by: >...

bednarsky

- [ ] https://github.com/nf-core/modules/issues/5064 - [ ] https://github.com/nf-core/modules/issues/5065 - [ ] https://github.com/nf-core/modules/issues/5066 - [ ] https://github.com/nf-core/modules/issues/5067 - [ ] https://github.com/nf-core/modules/issues/5068 - [ ] https://github.com/nf-core/modules/issues/5069 - [ ] https://github.com/nf-core/modules/issues/5070 - [...

Zethson

- [ ] Create a new nf-core branch - [ ] Recreate the the pipeline starting with the template - [ ] Add missing conda recipes #46 - [ ]...

Zethson

An attempt to run hadge with Singularity containers

3

Hello! Since our HPC does not work very well with conda, I tried to convert the hadge process-specific conda environments into Docker/Singularity containers and then run the workflow via Singularity....

kauralasoo

Hi I tried to figure this out but since i do not have an independent hash dataset to play with i am not sure if its test data dependent or...

maxozo

``` - name: Run pipeline with test data run: | nextflow run ${GITHUB_WORKSPACE} -profile test,conda --souporcell False --generate_anndata False ``` Currently we're only testing souporcell. Ideally, we should test all...

Zethson