Hi, does anyone know why I can’t pass the params y...
# pipeline-maintainersl
Lili Andersson-Li
12/08/2025, 1:14 PMHi, does anyone know why I can’t pass the params yaml file running the pipeline based the nf-core TEMPLATE
nextflow run genomic-medicine-sweden/metaval -r dev -profile singularity -params-file metaval_params_test.yml Copy code
Nextflow 25.10.2 is available - Please consider updating your version to it
N E X T F L O W ~ version 25.10.0
Cannot parse params file: metaval_params_test.ymla
Adrien Coulier
12/08/2025, 1:16 PMWhat is the content of your params file?
l
Lili Andersson-Li
12/08/2025, 1:18 PM Copy code
input:"samplesheet.csv"
outdir: "metaval_test"
pathogens_genomes: "reference/reference.fasta.gz"
accession2taxid: "reference/accession2taxid.map"
taxid2genome: "genomesdb/taxid2genome.map"
blastn_db: "blastDB/nt_viruses"
blastx_db: "diamond_db/diamond_representatives.dmnd"
perform_verify_species: True
extract_kraken2_reads: True
extract_centrifuge_reads: True
extract_diamond_reads: True
evalue_threshold: 1e-20
perform_shortread_denovo: True
perform_longread_denovo: True
min_read_counts: 20
blastn_min_qlen: 50
blastn_min_pident: 50
blastn_min_length: 50
blastn_max_evalue: 0.05
blastx_min_qlen: 50
blastx_min_pident: 50
blastx_min_length: 50
blastx_max_evalue: 0.05
perform_mapping: True
perform_screen_pathogens: True
perform_longread_consensus: True
perform_shortread_consensus: True
longread_consensus_tool: 'medaka'
consensus_min_bases: 50Lili Andersson-Li
12/08/2025, 1:19 PMI also tried using the json format and didn’t work either
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Adrien Coulier
12/08/2025, 1:21 PMWeird 🤔 Can you try adding a space between the column and the quote on line 1, i.e:
Copy code
input: "samplesheet.csv"l
Lili Andersson-Li
12/08/2025, 1:40 PMGood point! It’s working now after CHATGPT correcting the format. Thanks for the quick response!