command gen_read.py unknown

[LaporteF]

Hi,

I tried to use the first example (with a conda profile) and I ran into an error concerning the NEAT function gen_read.py.

nextflow run DIncalciLab/LFV-benchmark --input_all <input_csv> --outdir --bed <path_to_bed> --fasta --samples 2 --coverage 30 --type snv --high_sensitivity -profile conda

Command executed: gen_reads.py --bam --vcf --no-fastq --rng $RANDOM -r Homo_sapiens.GRCh38.fa -R 151 --pe-model /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/fraglenModel_default.pickle.gz -c 30 -e /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/errorModel_default.pickle.gz --gc-model /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/gcBias_default.pickle.gz -tr BedFile -m /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/MutModel_NA12878.pickle.gz -o neat_Sample1 samtools index neat_Sample1_golden.bam cat <<-END_VERSIONS > "neat_Sample1.versions.yml" "DINCALCILAB_LOWFRAC_VARIANT_BENCHMARK:LOWFRAC_VARIANT_BENCHMARK:NEAT": ncsa/NEAT: 'Version 3.2' GC bias model: /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/gcBias_default.pickle.gz Bed used: BedFile Mutational model: /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/MutModel_NA12878.pickle.gz FASTA: Homo_sapiens.GRCh38.fa Sequencing error model: /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/errorModel_default.pickle.gz Frag length model: /home/laporte-f/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/fraglenModel_default.pickle.gz Coverage: 30 Read length: 151 Meta: [sample_name:Sample1, info:null] END_VERSIONS Command exit status: 127 Command output: (empty) Command error: .command.sh: line 2: gen_reads.py: command not found

Do I have to install NEAT first ?

Regard

[lbeltrame]

Hello,

The key is in -profile conda from your command line. So far only an approach which goes through Docker is supported.