nf-core/detaxizer

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

detaxizer's Issues

Project config file is malformed

Description of the bug

Nextflow 20.10.0 complains that the config is malformed when I do not specify a config file. The .nextflow.log (see below) hints at the provided nextflow.config, but I can't spot the issue.

The sample sheet is in csv format with three columns as described in the usage documentation

Expected: normal pipeline run.

Command used and terminal output

$ nextflow run nf-core/detaxizer --input samplesheet.csv --outdir results/detaxizer

N E X T F L O W  ~  version 20.10.0
Pulling nf-core/detaxizer ...
Project config file is malformed -- Cause: No signature of method: nextflow.config.ConfigParser$_parse_closure5.id() is applicable for argument types: (String) values: [[email protected]]
Possible solutions: is(java.lang.Object), is(java.lang.Object), find(), find(), find(groovy.lang.Closure), find(groovy.lang.Closure)

Relevant files

.nextflow.log:

Jan-30 15:54:32.091 [main] INFO  nextflow.cli.CmdRun - Pulling nf-core/detaxizer ...
Jan-30 15:54:32.092 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/detaxizer/contents/nextflow.config
Jan-30 15:54:33.089 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.Exception: Project config file is malformed -- Cause: No signature of method: nextflow.config.ConfigParser$_parse_closure5.id() is applicable for argument types: (String) values: [[email protected]]

System information

Nextflow 20.10.0
Hardware: HPC
Executor: Tried Slurm, but also get the issue locally
No container
OS: Ubuntu
There is no detaxizer version yet

Supporting multiple taxons with tax2filter

Description of feature

The current version of tax2filter only allows the filtering out of a single taxon. However, it would be more useful if it could support multiple taxons separated by either a comma or semicolon. In my metagenomics project, I need to filter out human, bacteria, and archaea. Unfortunately, the current version of detaxizer does not permit filtering out all three taxons in one pipeline run.

tax2filter doesnt accept arguments with blank

Description of the bug

I wanted to retain from some samples only plasmid and virus sequences, so I used --tax2filter "cellular organisms" but that failed (see below). I assume that could be fixed by changing
parse_kraken2report.py -i $kraken2report -t $params.tax2filter
to
parse_kraken2report.py -i $kraken2report -t "$params.tax2filter"

Command used and terminal output

NXF_VER=23.10.1 nextflow run nf-core/detaxizer -r 1.0.0 -profile cfc --input samplesheet_detaxizer.csv --kraken2db https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240112.tar.gz --tax2filter "cellular organisms" --skip_blastn --enable_filter --filter_with_kraken2 --cutoff_tax2keep 0.1 --cutoff_tax2filter 0 --cutoff_unclassified 0.0 --outdir detaxizer


nf-core/detaxizer execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 2.

The full error message was:

Error executing process > 'NFCORE_DETAXIZER:DETAXIZER:PARSE_KRAKEN2REPORT (BAC89)'

Caused by:
  Process `NFCORE_DETAXIZER:DETAXIZER:PARSE_KRAKEN2REPORT (BAC89)` terminated with an error exit status (2)

Command executed:

  parse_kraken2report.py -i BAC89.kraken2.report.txt -t cellular organisms
  
  cat  versions.yml
  "NFCORE_DETAXIZER:DETAXIZER:PARSE_KRAKEN2REPORT":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  usage: parse_kraken2report.py [-h] -i INPUT -t TAX2FILTER
  parse_kraken2report.py: error: unrecognized arguments: organisms

Work dir:
  /sfs/9/ws/bcgsd01-QAPXD_24-05-16/detaxized/work/95/9d56dec3696104cf4604460468e1c9

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Relevant files

No response

System information

No response