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println("""-profile [STRING] What profile should be used to run the workflow. Options are [singularity, docker, conda, slurm_sing, slurm_conda].
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println("""-profile [STRING] What profile should be used to run the workflow. Options are [singularity, docker, conda, slurm].
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singularity, docker and conda will run the pipelne locally using singularity, docker, and conda, respectively.
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slurm_sing and slurm_conda will submit and run jobs using slurm in singularity containers and conda environments, respectively. """)
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To combine profiles, pass them together separated by comma. For example, to run jobs using slurm in singularity containers use 'slurm,singularity' . """)
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println("--csv_file [PATH] A 3-column (single-end) or 4-column (paired-end) input file (sample_id, forward, [reverse,] paired). Mandatory if a GLDS accession is not provided.")
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println(" Please see the files: SE_file.csv and PE_file.csv for single-end and paired-end examples, respectively.")
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println(" The sample_id column should contain unique sample ids.")
@@ -38,22 +37,22 @@ if (params.help) {
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println("PLEASE NOTE: This workflow assumes that all your raw reads end with the same suffix. If they don't please modify your filenames to have the same suffix as shown below.")
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println("--raw_R1_suffix [STRING] Raw forward reads suffix (region following the unique part of the sample names). e.g. _R1_raw.fastq.gz.")
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println("--raw_R2_suffix [STRING] Raw reverse reads suffix (region following the unique part of the sample names). e.g. _R2_raw.fastq.gz.")
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println()
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println("Cutadapt (trimming) parameters:")
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println(" --F_primer [STRING] Forward primer sequence e.g. AGAGTTTGATCCTGGCTCAG. Default: emptry string.")
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println(" --R_primer [STRING] Reverse primer sequence e.g. CTGCCTCCCGTAGGAGT. Default: emptry string.")
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println(" --min_cutadapt_len [INTEGER] What should be the minimum read length after quality trimming with cutadapt. Default: 130.")
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println(" --primers_linked [STRING] Are the primers linked?. https://cutadapt.readthedocs.io/en/stable/recipes.html#trimming-amplicon-primers-from-paired-end-reads. Default: TRUE. ")
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println(" --discard_untrimmed [STRING] Should untrimmed reads be discarded? Any supplied string except TRUE will not discard them. Default: TRUE.")
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println()
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println("Optional arguments:")
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println(" --help Print this help message and exit.")
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println(" --publishDir_mode [STRING] How should nextflow publish file outputs. Options can be found here https://www.nextflow.io/docs/latest/process.html#publishdir. Default: link.")
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println(" --errorStrategy [STRING] How should nextflow handle errors. Options can be found here https://www.nextflow.io/docs/latest/process.html#errorstrategy. Default: terminate")
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println(" --enable_visualizations [BOOLEAN] Should ASV plots be made? true or false. if true supply a path to the ruhnsheet for plotting to the --runsheet option. Default: false.")
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println(" --runsheet [PATH] A 4-column file with these exact headers [Sample Name, read1_path, raw_R1_suffix, groups] for plotting. Only relevant if --enable_visualizations is true. Default: null.")
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println(" --multiqc_config [PATH] Path to a custome multiqc config file. Default: config/multiqc.config.")
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println()
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println("Dada2 parameters passed to filterAndTrim() function:")
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println(" --left_trunc [INTEGER] truncate the sequences to the left by this number of bases. Default: 0.")
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println(" --right_trunc [INTEGER] truncate the sequences to the right by this number of bases. Default: 0.")
@@ -63,13 +62,12 @@ if (params.help) {
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println(" This is typically used with primers like 515-926, that captured 18S fragments that are typically too long to merge.")
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println(" Note that 16S and 18S should have been separated already prior to running this workflow. This should likely be left as FALSE for any option other than 18S above.")
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println(" Values are TRUE or FALSE Default: FALSE.")
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println()
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println("File Suffixes:")
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println(" --primer_trimmed_R1_suffix [STRING] Suffix to use for naming your primer trimmed forward reads. Default: _R1_trimmed.fastq.gz.")
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println(" --primer_trimmed_R2_suffix [STRING] Suffix to use for naming your primer trimmed reverse reads. Default: _R2_trimmed.fastq.gz.")
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println(" --filtered_R1_suffix [STRING] Suffix to use for naming your quality filtered forward reads. Default: _R1_filtered.fastq.gz.")
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println(" --filtered_R2_suffix [STRING] Suffix to use for naming your quality filtered reverse reads. Default: _R2_filtered.fastq.gz.")
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println()
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println("Output directories:")
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println(" --raw_reads_dir [PATH] Where should the fastqc report of the raw reads be stored. Default: Raw_Sequence_Data/.")
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println(" --fastqc_out_dir [PATH] Where should multiqc outputs be stored. Default: workflow_output/FastQC_Outputs/.")
@@ -78,12 +76,10 @@ if (params.help) {
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println(" --info_out_dir [PATH] Where should output metadata be stored. Default: workflow_output/Metadata/.")
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println(" --plots_dir [PATH] Where should your plots be stored if visualization is enabled. Default: workflow_output/Final_Outputs/Plots/.")
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println(" --final_outputs_dir [PATH] Where should most outputs and summary reports be stored. Default: workflow_output/Final_Outputs/.")
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println()
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println("Genelab specific arguements:")
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println(" --GLDS_accession [STRING] A Genelab accession number if the --csv_file parameter is not set. If this parameter is set, it will ignore the --csv_file parameter.")
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