Hi, I'm had a hard time to get things running in a new project. My old project uses nextflow 25.10.5 and works fine. After setting up nextflow the new project (26.04.1) I get the following errors: tried both 5.4.2 and dev. Also tried

--skip_spades false

etc. for the failing params. Switching back to 25.10.5 worked for me with dev and 5.4.2. I guess this is a nextflow thingy.

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --skip_spades (true): Value is [string] but should be [boolean]
* --run_virus_identification (true): Value is [string] but should be [boolean]
* --run_checkm2 (true): Value is [string] but should be [boolean]
* --refine_bins_dastool (true): Value is [string] but should be [boolean]

nextflow run nf-core/mag -r dev\
   --input ${METADATA} \
   --outdir ${OUTPUTDIR} \
   --host_fasta ${HOSTFASTA} \
   --host_fasta_bowtie2index ${HOSTBOWTIE2_INDEX} \
   --gtdb_db ${DATABASEDIR}/gtdb/release226 \
   --bin_domain_classifications \
   --checkm2_db ${CHECKM2DB} \
   --run_checkm2 \
   --email ${EMAIL} \
   --skip_spades \
   --run_virus_identification \
   --genomad_db ${GENOMEADDIR} \
   --refine_bins_dastool \
   --postbinning_input both \
   --max_cpus ${SLURM_JOB_CPUS_PER_NODE} \
   -profile apptainer \
   -work-dir ${WORKDIRPROJECT} \
   -c ${PIPELINECONFIGDIR}/mag.snelliusnode_${SLURM_JOB_CPUS_PER_NODE}.conf \
   -resume

New nextflow releases come with changes that cannot always anticipated fully. The pipeline is buildt with the (usually) latest nextfow version that was available at the time. Just check out the github page, the readme mentions the minimum nextflow version. This version was tested by CI tests and therefore is reliably working even for ancient pipeline versions. Thats true for all nf-core pipelines. Just use e.g.

NXF_VER=25.04.2 nextflow run nf-core/mag -r 5.4.2 <...>

and the chosen nxf version will be used. No need to install anything. I always recommend to fix both on the command line, the nextflow version and the pipeline version.