strict-syntax-health/lint_results/prints-help-results/chipseq_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 26.03.1-edge

Downloading plugin nf-schema@2.5.1
Launching `./main.nf` [agitated_brenner] revision: 68c857869d

WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/chipseq 2.2.0dev
------------------------------------------------------
Typical pipeline command:

  nextflow run nf-core/chipseq -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>

help message of that parameter will be printed.
or `--helpFull`.

Input/output options
  --input                       [string]  Path to comma-separated file containing information about the samples in the experiment.
  --fragment_size               [integer] Estimated fragment size used to extend single-end reads. [default: 200]
  --seq_center                  [string]  Sequencing center information to be added to read group of BAM files.
  --read_length                 [integer] Read length used to calculate MACS3 genome size for peak calling if `--macs_gsize` isn't provided.
 (accepted: 50, 75, 100, 150, 200)
  --outdir                      [string]  The output directory where the results will be saved. You have to use absolute paths to storage on
Cloud infrastructure.
  --email                       [string]  Email address for completion summary.
  --multiqc_title               [string]  MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Reference genome options
  --genome                      [string]  Name of iGenomes reference.
  --fasta                       [string]  Path to FASTA genome file.
  --gtf                         [string]  Path to GTF annotation file.
  --gff                         [string]  Path to GFF3 annotation file.
  --bwa_index                   [string]  Path to directory or tar.gz archive for pre-built BWA index.
  --bowtie2_index               [string]  Path to directory or tar.gz archive for pre-built Bowtie2 index.
  --chromap_index               [string]  Path to directory or tar.gz archive for pre-built Chromap index.
  --star_index                  [string]  Path to directory or tar.gz archive for pre-built STAR index.
  --gene_bed                    [string]  Path to BED file containing gene intervals. This will be created from the GTF file if not specified.

  --macs_gsize                  [number]  Effective genome size parameter required by MACS3.
  --blacklist                   [string]  Path to blacklist regions in BED format, used for filtering alignments.
  --save_reference              [boolean] If generated by the pipeline save the BWA index in the results directory.

Adapter trimming options
  --clip_r1                     [integer] Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
  --clip_r2                     [integer] Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
  --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.
  --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.
  --trim_nextseq                [integer] Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing
poly-G tails.
  --skip_trimming               [boolean] Skip the adapter trimming step.
  --save_trimmed                [boolean] Save the trimmed FastQ files in the results directory.

Alignment options
  --aligner                     [string]  Specifies the alignment algorithm to use - available options are 'bwa', 'bowtie2' and 'star'.
(accepted: bwa, bowtie2, chromap, star) [default: bwa]
  --keep_dups                   [boolean] Duplicate reads are not filtered from alignments.
  --keep_multi_map              [boolean] Reads mapping to multiple locations are not filtered from alignments.
  --bwa_min_score               [integer] Don’t output BWA MEM alignments with score lower than this parameter.
  --save_align_intermeds        [boolean] Save the intermediate BAM files from the alignment step.
  --save_unaligned              [boolean] Save unaligned sequences to the output directory (only available for Bowtie 2 and STAR.

Peak calling options
  --narrow_peak                 [boolean] Run MACS3 in narrowPeak mode.
  --broad_cutoff                [number]  Specifies broad cutoff value for MACS3. Only used when --narrow_peak isnt specified. [default:
0.1]
  --macs_fdr                    [number]  Minimum FDR (q-value) cutoff for peak detection, --macs_fdr and --macs_pvalue are mutually
exclusive.
  --macs_pvalue                 [number]  p-value cutoff for peak detection, --macs_fdr and --macs_pvalue are mutually exclusive. If
--macs_pvalue cutoff is set, q-value will not be calculated and reported as -1 in the final .xls
file.
  --min_reps_consensus          [integer] Number of biological replicates required from a given condition for a peak to contribute to a
consensus peak. [default: 1]
  --save_macs_pileup            [boolean] Instruct MACS3 to create bedGraph files normalised to signal per million reads.
  --skip_peak_qc                [boolean] Skip MACS3 peak QC plot generation.
  --skip_peak_annotation        [boolean] Skip annotation of MACS3 and consensus peaks with HOMER.
  --skip_consensus_peaks        [boolean] Skip consensus peak generation, annotation and counting.

Process skipping options
  --skip_fastqc                 [boolean] Skip FastQC.
  --skip_picard_metrics         [boolean] Skip Picard CollectMultipleMetrics.
  --skip_preseq                 [boolean] Skip Preseq.
  --deseq2_vst                  [boolean] Use vst transformation instead of rlog with DESeq2. [default: true]
  --skip_plot_profile           [boolean] Skip deepTools plotProfile.
  --skip_plot_fingerprint       [boolean] Skip deepTools plotFingerprint.
  --skip_spp                    [boolean] Skip Phantompeakqualtools.
  --skip_deseq2_qc              [boolean] Skip DESeq2 PCA and heatmap plotting.
  --skip_igv                    [boolean] Skip IGV.
  --skip_multiqc                [boolean] Skip MultiQC.
  --skip_qc                     [boolean] Skip all QC steps except for MultiQC.

Generic options
  --multiqc_methods_description [string]          Custom MultiQC yaml file containing HTML including a methods description.
  --help                        [boolean, string] Display the help message.
  --help_full                   [boolean]         Display the full detailed help message.
  --show_hidden                 [boolean]         Display hidden parameters in the help message (only works when --help or --help_full are provided).

 !! Hiding 23 param(s), use the `--showHidden` parameter to show them !!
------------------------------------------------------

* The pipeline
    https://doi.org/10.5281/zenodo.3240506

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

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