Command not found

[cjw85]

          @nrhorner 

Is there any documentation error about Differential Expression?

wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
OUTPUT=~/output;
nextflow run epi2me-labs/wf-transcriptomes \
  --fastq  differential_expression/differential_expression_fastq \
  --de_analysis \
  --ref_genome differential_expression/hg38_chr20.fa \
  --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
  --direct_rna --minimap2_index_opts \
  -k15

Error message Unknown option: -k15 -- Check the available commands and options and syntax with 'help'

nextflow run epi2me-labs/wf-transcriptomes --fastq differential_expression/differential_expression_fastq --de_analysis --ref_genome differential_expression/hg38_chr20.fa --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf --direct_rna --minimap2_index_opts

Error message N E X T F L O W ~ version 23.04.1 Launching https://github.com/epi2me-labs/wf-transcriptomes [goofy_kilby] DSL2 - revision: fcc7347a8b [master]

ERROR ~ ERROR: Validation of pipeline parameters failed!

-- Check '.nextflow.log' file for details ERROR ~ * --minimap2_index_opts: expected type: String, found: Boolean (true)

-- Check '.nextflow.log' file for details ERROR ~ * Missing parameter(s) that are required by --de_analysis: --sample_sheet

-- Check '.nextflow.log' file for details

WARN: Found unexpected parameters:

• --version: false
• Ignore this warning: params.schema_ignore_params = "version"

nextflow run epi2me-labs/wf-transcriptomes --fastq differential_expression/differential_expression_fastq --de_analysis --ref_genome differential_expression/hg38_chr20.fa --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf --direct_rna --minimap2_index_opts --sample_sheet sample_sheet.csv

Error message N E X T F L O W ~ version 23.04.1 Launching https://github.com/epi2me-labs/wf-transcriptomes [peaceful_ptolemy] DSL2 - revision: fcc7347a8b [master]

ERROR ~ ERROR: Validation of pipeline parameters failed!

-- Check '.nextflow.log' file for details ERROR ~ * --minimap2_index_opts: expected type: String, found: Boolean (true)

-- Check '.nextflow.log' file for details

WARN: Found unexpected parameters:

• --version: false
• Ignore this warning: params.schema_ignore_params = "version"

Originally posted by @yucenwan00 in https://github.com/epi2me-labs/wf-transcriptomes/issues/28#issuecomment-1705877259

[nrhorner]

That command looks to from some older documentation.

The command from the current README is

  --fastq  differential_expression/differential_expression_fastq \
  --de_analysis \
  --transcriptome_source precomputed \
  --ref_genome differential_expression/hg38_chr20.fa \
  --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
  --direct_rna --minimap2_index_opts '-k 15' \
  --ref_transcriptome differential_expression/ref_transcriptome.fasta \
  --sample_sheet test_data/sample_sheet.csv```