Comments (9)
removed obvious problems but unzip
still doesnt work
from ampliseq.
That just requires to add conda-forge::unzip=6.0
to our environment.yaml
and we're all good :-)
from ampliseq.
works when I use my QIIME2 conda environment, but doesnt work with --profile singularity
:
.command.sh: line 2: unzip: command not found
from ampliseq.
Probably outdated container -it doesn#t download the updated one from yesterday if there is one present in your work/singularity/...
folder :-)
from ampliseq.
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"
from ampliseq.
Super weird, restarted the docker cloud build.
from ampliseq.
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 :-)
from ampliseq.
This fixes the issue locally - test it on the cluster and let me know how it goes :-)
from ampliseq.
Build finished, testing works and unzip is found :-)
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Related Issues (20)
- Adding the new Greengenes2 database for classification HOT 2
- Phyloseq object creation will fail if any samples have all reads removed by the tax filtering step HOT 5
- Add blast-consensus support to Ampliseq HOT 1
- Add greengenes2 2022.10 support to Ampliseq HOT 1
- Add custom qiime reference database support to Ampliseq. HOT 2
- Edge case: Clustering with VSEARCH fails at QIIME2_INSEQ HOT 1
- Allow to analyse 454 sequencing data HOT 2
- Add option to assign ASV to multiple species with DADA2 HOT 3
- Debug information for docker-based run. HOT 4
- Allow stratified output from picrust2 HOT 4
- nf-core/ampliseq with conda - change bioconductor-biostrings HOT 2
- Launch webpage not working HOT 4
- Adding qza file for downstream analysis in R HOT 3
- When using `--vsearch_cluster`, if you have many thousands of clusters, `AMPLISEQ:FILTER_CLUSTERS` will fail with an `Argument list too long` error. HOT 8
- test_full Cannot access file fastq HOT 1
- Multipe region amplicon sequencing analysis support (5R / SMURF / q2-sidle) HOT 1
- Getting ca 50% more ASVs than when using DADA2 on QIIME2 HOT 2
- ampliseq fails during taxonomy assignation when processing ITS sequences HOT 14
- Error No subject alternative DNS name matching zenodo.org found HOT 2
- minor improvement of sort() before denoising with method = "radix HOT 2
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