Run cannot start due to "Unknown option"

[mpiersonsmela]

Description of the bug

Whenever I try running the pipeline, it gives an "unknown option" error. The "--help" option works OK though.

Command used and terminal output

Command:

nextflow run nf-core/cutandrun -—input ./test-GSE145187-all-small.csv --peakcaller seacr,macs2 --genome GRCh38 --outdir output -profile conda

Output:

Unknown option: -—input -- Check the available commands and options and syntax with 'help'

Command:

nextflow run nf-core/cutandrun -—input test-GSE145187-all-small.csv --outdir output -profile conda

Output:

Unknown option: -—input -- Check the available commands and options and syntax with 'help'


Command:

nextflow run nf-core/cutandrun --help

Output:

N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/cutandrun` [cheeky_carson] DSL2 - revision: 6e1125d4fe [master]


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/cutandrun v3.2.2-g6e1125d
------------------------------------------------------
Typical pipeline command:

  nextflow run nf-core/cutandrun --input samplesheet.csv --genome GRCh37 -profile docker

Input/output options
  --input                             [string]  Path to comma-separated file containing information about the samples in the experiment.
  --outdir                            [string]  The output directory where the results will be saved. You have to use absolute paths to store on Cloud 
                                                infrastructure. [default: ./results] 
  --multiqc_title                     [string]  MultiQC report title. Printed as page header, used for filename if not otherwise specified.
  --save_reference                    [boolean] Save genome reference data to the output directory
  --save_merged_fastq                 [boolean] Save any technical replicate FASTQ files that were merged to the output directory
  --save_trimmed                      [boolean] Save trimmed FASTQ files to the output directory
  --save_spikein_aligned              [boolean] Save BAM files aligned to the spike-in genome to the output directory
  --save_unaligned                    [boolean] Save unaligned sequences to the output directory
  --save_align_intermed               [boolean] Save alignment intermediates to the output directory (WARNING: can be very large)
  --email                             [string]  Email address for completion summary.
  --dump_scale_factors                [boolean] Output calculated scale factors from pipeline

Reference data options
  --genome                            [string]  Name of iGenomes reference.
  --bowtie2                           [string]  Path to bowtie2 index
  --gtf                               [string]  Path to GTF annotation file
  --gene_bed                          [string]  Path to gene BED file
  --blacklist                         [string]  Path to genome blacklist
  --spikein_genome                    [string]  Name of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for 
                                                fruit fly BDGP6 [default: K12-MG1655] 
  --spikein_bowtie2                   [string]  Path to spike-in bowtie2 index
  --spikein_fasta                     [string]  Path to spike-in fasta
  --fasta                             [string]  Path to FASTA genome file.

Flow switching options
  --only_input                        [boolean] Run pipeline up to input checking
  --only_genome                       [boolean] Run pipeline up to reference preparation
  --only_preqc                        [boolean] Run pipeline up to pre-alignment
  --only_alignment                    [boolean] Run pipeline up to alignment
  --only_filtering                    [boolean] Run pipeline up to q-filtering
  --only_peak_calling                 [boolean] Run pipeline up to peak calling
  --skip_fastqc                       [boolean] Skips fastqc reporting
  --skip_trimming                     [boolean] Skips trimming
  --skip_removeduplicates             [boolean] Skips de-duplication
  --skip_reporting                    [boolean] Skips reporting
  --skip_preseq                       [boolean] Skips preseq reporting
  --skip_igv                          [boolean] Skips igv session generation
  --skip_dt_qc                        [boolean] Skips deeptools QC repoting
  --skip_heatmaps                     [boolean] Skips deeptools heatmap generation
  --skip_peak_qc                      [boolean] Skips peak QC reporting
  --skip_multiqc                      [boolean] Skips multiqc

Trimming Options
  --clip_r1                           [integer] Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads). [default: 0]
  --clip_r2                           [integer] Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only). [default: 0]
  --three_prime_clip_r1               [integer] Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been 
                                                performed. [default: 0] 
  --three_prime_clip_r2               [integer] Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been 
                                                performed. [default: 0] 
  --trim_nextseq                      [integer] Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails. 
                                                [default: 0] 

Pipeline Options
  --minimum_alignment_q_score         [integer] Filter reads below a q-score threshold [default: 20]
  --remove_mitochondrial_reads        [boolean] Filter mitochondrial reads
  --mito_name                         [string]  Name of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference 
                                                genome. 
  --dedup_target_reads                [boolean] De-duplicate target reads AND control reads (default is control only)
  --remove_linear_duplicates          [boolean] De-duplicate reads based on read 1 5' start position. Relevant for assays using linear amplification with 
                                                tagmentation (default is false). 
  --end_to_end                        [boolean] Use --end-to-end mode of Bowtie2 during alignment [default: true]
  --normalisation_mode                [string]  Sets the target read normalisation mode. Options are: ["Spikein", "RPKM", "CPM", "BPM", "None" ] (accepted: 
                                                Spikein, RPKM, CPM, BPM, None) [default: Spikein] 
  --normalisation_binsize             [integer] If normsalisation option is one of  "RPKM", "CPM", "BPM" - then the binsize that the reads count is calculated 
                                                on is used. [default: 50] 
  --peakcaller                        [string]  Selects the peak caller for the pipeline. Options are: [seacr, macs2]. More than one peak caller can be chosen 
                                                and the order specifies which is a primary peak called (the first) that will be used downstream. Any secondary 
                                                peak callers will be run and outputed to the results folder. [default: seacr] 
  --use_control                       [boolean] Specifies whether to use a control to normalise peak calls against (e.g. IgG) [default: true]
  --extend_fragments                  [boolean] Specifies whether to extend paired-end fragments between the read mates when calculating coveage tracks 
                                                [default: true] 
  --igg_scale_factor                  [number]  Specifies whether the background control is scaled prior to being used to normalise peaks. [default: 
                                                0.5] 
  --seacr_peak_threshold              [number]  SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This 
                                                is only used if there are no controls included with the samples and if `--use_control` is `false` [default: 
                                                0.05] 
  --seacr_norm                        [string]  SEACR normalization.  (accepted: non, norm) [default: non]
  --seacr_stringent                   [string]  SEACR stringency. (accepted: stringent, relaxed) [default: stringent]
  --macs2_qvalue                      [number]  Q-value threshold for MACS2 peak caller. [default: 0.01]
  --macs2_pvalue                      [number]  P-value threshold for macs2 peak caller. If set it will overide the qvalue.
  --macs_gsize                        [number]  parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as 
                                                *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the 
                                                gsize will default to GRCh38. [default: 2700000000] 
  --macs2_narrow_peak                 [boolean] Determines whether MACS2 broad or narrow peak mode is used for the peak caller [default: true]
  --macs2_broad_cutoff                [number]  MACS2 broad cutoff parameter [default: 0.1]
  --consensus_peak_mode               [string]  Specifies what samples to group together for consensus peaks. Options are [group, all] (accepted: group, 
                                                all) [default: group] 
  --replicate_threshold               [number]  Minimum number of overlapping replicates needed for a consensus peak [default: 1]
  --igv_show_gene_names               [boolean] Show gene names instead of symbols in IGV browser sessions [default: true]

Reporting Options
  --dt_qc_bam_binsize                 [integer] Deeptools multiBamSummary bam bin size [default: 500]
  --dt_qc_corr_method                 [string]  Deeptools Correlation Plot statistical calculation method [default: pearson]
  --dt_heatmap_gene_beforelen         [integer] Deeptools heatmap gene plot before length (bases) [default: 3000]
  --dt_heatmap_gene_bodylen           [integer] Deeptools heatmap gene plot body length (bases) [default: 5000]
  --dt_heatmap_gene_afterlen          [integer] Deeptools heatmap gene plot after length (bases) [default: 3000]
  --dt_heatmap_peak_beforelen         [integer] Deeptools heatmap peak plot before length (bases) [default: 3000]
  --dt_heatmap_peak_afterlen          [integer] Deeptools heatmap peak plot after length (bases) [default: 3000]
  --dt_calc_all_matrix                [boolean] Flag for whether to generate a heatmap for all samples together [default: true]
  --min_frip_overlap                  [number]  Minimum fragment overlap for FriP score [default: 0.2]
  --min_peak_overlap                  [number]  Minimum peak overlap for peak reproducibility plot [default: 0.2]
  --igv_sort_by_groups                [boolean] Sort the IGV output tracks by group [default: true]

Generic options
  --singularity_pull_docker_container [boolean] Pull Docker container.
  --multiqc_methods_description       [string]  Custom MultiQC yaml file containing HTML including a methods description.

 !! Hiding 26 params, use --validationShowHiddenParams to show them !!
------------------------------------------------------
If you use nf-core/cutandrun for your analysis please cite:

  https://doi.org/10.5281/zenodo.5653535

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/cutandrun/blob/master/CITATIONS.md

Relevant files

No response

System information

Nextflow version 23.10.1

Hardware: HPC

Executor: local and slurm

Container: Conda

Version: nf-core/cutandrun v3.2.2-g6e1125d

[mpiersonsmela]

I am still having this problem, are the developers looking into it?

[mpiersonsmela]

nextflow.log
Here is my .nextflow.log file.

[mpiersonsmela]

This was caused by a dumb mistake with dashes and hyphens.