strict-syntax-health/lint_results/prints-help-results/alleleexpression_help.txt at main · nf-core/strict-syntax-health · GitHub

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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help


 N E X T F L O W   ~  version 25.12.0-edge

Downloading plugin nf-validation@1.1.3
Launching `./main.nf` [festering_elion] DSL2 - revision: 3f717d2232

alleleexpression pipeline parameters:
  --help=true
  --input=null
  --outdir=null
  --chromosome=chr11
  --genome=null
  --fasta=null
  --gtf=null
  --star_index=null
  --gene_features=null
  --beagle_ref=null
  --beagle_map=null
  --umi_separator=:
  --max_cpus=16
  --max_memory=128.GB
  --max_time=240.h
  --publish_dir_mode=copy
  --email=null
  --email_on_fail=null
  --plaintext_email=false
  --monochrome_logs=false
  --hook_url=null
  --version=false
  --validate_params=true
  --show_hidden_params=false
  --schema_ignore_params=genomes,modules
  --modules=null
  --multiqc_config=null
  --multiqc_title=null
  --multiqc_logo=null
  --max_multiqc_email_size=25.MB
  --tracedir=null/pipeline_info
  --igenomes_base=s3://ngi-igenomes/igenomes/
  --igenomes_ignore=false
  --custom_config_version=master
  --custom_config_base=https://raw.githubusercontent.com/nf-core/configs/master
  --config_profile_description=null
  --config_profile_contact=null
  --config_profile_url=null
  --config_profile_name=null
  --genomes=[GRCh37:[fasta:s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa, bwa:s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa, bowtie2:s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/, star:s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/, gtf:s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf, bed12:s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed], GRCh38:[fasta:s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa, bwa:s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa, bowtie2:s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/, star:s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/, gtf:s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf, bed12:s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed], GRCm38:[fasta:s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa, bwa:s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa, bowtie2:s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/, star:s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/, gtf:s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf, bed12:s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed]]
Input samplesheet not specified!