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