clustering_thresholds for 16S pipeline expect 2 or more comma seperated values and fails for a single value

[scleveland]

The 16s pipeline will fail if a user inputs just 100 for the Mothur OTU clustering threshold parameter. The code attempts to run a "split" on the paramter which will fail for a single threshold value. Perhaps it should be updated to check for the presence of a comma in the string before running the "split" and if not found set the threshold value to the string input without splitting.

[Puumanamana]

I thought I tested that before, but I guess not, or could be a version issue Maybe changing from .split(',') to .tokenize(',') would solve it, I've gotten unexpected results with .split() in the past

[Puumanamana]

I can confirm that running the 16S pipeline works locally on my VM (Linux). Here's the command and my configuration:

nextflow run Pipeline-16S -w testrun/work -resume -profile local,docker,test16S --outdir testrun/16S --clustering_thresholds 100

$ nextflow -version                                                                                                                                                                    1 ↵

      N E X T F L O W
      version 23.04.4 build 5881
      created 25-09-2023 15:34 UTC
      cite doi:10.1038/nbt.3820
      http://nextflow.io

$ java -version
openjdk version "17.0.9" 2023-10-17
OpenJDK Runtime Environment (build 17.0.9+9-Debian-1deb11u1)
OpenJDK 64-Bit Server VM (build 17.0.9+9-Debian-1deb11u1, mixed mode, sharing)

[gadepallivs]

Hi, Followed the documentation for the Microbial 16S pipeline, but could not run the pipeline. Any inputs will be helpful

git clone https://github.com/hawaiidatascience/metaflowmics.git
mkdir -p databases/silva/v138 && cd databases/silva/v138
wget https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v138.tgz
tar -xvzf silva.nr_v138.tgz && rm -f silva.nr_v138.tgz

then

nextflow run 16S-pipeline -profile <config> --reads fastq_data_metabolomics/*_R{1,2}*.fastq* --referenceAln databases/silva/v138/silva.nr_v138.align --referenceTax databases/silva/v138/silva.nr_v138.tax I get the following error

N E X T F L O W ~ version 23.10.0 Pulling nextflow-io/16S-pipeline ... WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/nextflow-io/16S-pipeline/contents/nextflow.config Remote resource not found: https://api.github.com/repos/nextflow-io/16S-pipeline/contents/main.nf

[Puumanamana]

Hi, You need to use the path to the pipeline-16S folder, so here it looks like it should be: nextflow run metaflowmics/metaflowmics/pipeline-16S ...