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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
187 stars 117 forks source link

Missing "unzip" in the silva classifier step #35

Closed d4straub closed 6 years ago

d4straub commented 6 years ago

Process make_SILVA_132_16S_classifier slipped our test runs. Test command for fast processing e.g.: nextflow run rrna-ampliseq -profile test,singularity --classifier false --dereplication 90

from #33

d4straub commented 6 years ago

removed obvious problems but unzip still doesnt work

apeltzer commented 6 years ago

That just requires to add conda-forge::unzip=6.0 to our environment.yaml and we're all good :-)

d4straub commented 6 years ago

works when I use my QIIME2 conda environment, but doesnt work with --profile singularity: .command.sh: line 2: unzip: command not found

apeltzer commented 6 years ago

Probably outdated container -it doesn#t download the updated one from yesterday if there is one present in your work/singularity/... folder :-)

d4straub commented 6 years ago

Locally with recently pulled github repo, deleted folders work and .nextflow and run

nextflow run rrna-ampliseq -profile test,singularity --classifier false --dereplication 90 --skip_fastqc --skip_ancom --skip_diversity_indices --skip_alpha_rarefaction

but still ".command.sh: line 2: unzip: command not found"

apeltzer commented 6 years ago

Super weird, restarted the docker cloud build.

apeltzer commented 6 years ago

Ah, I see - pipeline uses latest, change is only present on dev. I'm pushing to master to force a container update here as well and then we're good :-)

apeltzer commented 6 years ago

This fixes the issue locally - test it on the cluster and let me know how it goes :-)

apeltzer commented 6 years ago

Build finished, testing works and unzip is found :-)