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commandline_messages.nf
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#!/usr/bin/env nextflow
ANSI_GREEN = "\033[1;32m"
ANSI_RED = "\033[1;31m"
ANSI_RESET = "\033[0m"
/*
========================================================================================
PRINT PARAMETER SUMMARY
========================================================================================
*/
def parameter_Message(){
if(params.pipeline === 'bacass'){
params.plas_assemblies = 'not used'
params.plas_outdir = 'not used'
} else if ((params.pipeline === 'plasmident') ||(params.pipeline === 'unicycler')){
params.samplesheet_header = 'not used'
params.genomesize = 'not used'
}
if (params.reads === 'short'){
params.ont_reads_input = 'not used'
params.ont_reads_outdir = 'not used'
}else if (params.reads === 'long'){
params.int_reads_input = 'not used'
}
log.info """
===========================================
${ANSI_GREEN}Sample sheet generator for various pipelines${ANSI_RESET}
Used parameters:
-------------------------------------------
--pipeline : ${params.pipeline}
--reads : ${params.reads}
--mapping_file : ${params.mapping_file}
--outdir : ${params.outdir}
--multiqc_config : ${params.multiqc_config}
Illumina options:
-------------------------------------------
--int_reads_input : ${params.int_reads_input}
Nanopore options:
-------------------------------------------
--ont_reads_input : ${params.ont_reads_input}
--ont_reads_outdir : ${params.ont_reads_outdir}
Nf-core/bacass or /viralrecon options:
-------------------------------------------
--samplesheet_header : ${params.samplesheet_header}
--genomesize : ${params.genomesize}
plasmIDent options:
-------------------------------------------
--plas_assemblies : ${params.plas_assemblies}
--plas_outdir : ${params.plas_outdir}
Runtime data:
-------------------------------------------
Running with profile : ${ANSI_GREEN}${workflow.profile}${ANSI_RESET}
Used container : ${ANSI_GREEN}${workflow.container}${ANSI_RESET}
Running as user : ${ANSI_GREEN}${workflow.userName}${ANSI_RESET}
Launch dir : ${ANSI_GREEN}${workflow.launchDir}${ANSI_RESET}
Base dir : ${ANSI_GREEN}${baseDir}${ANSI_RESET}
Nextflow version : ${ANSI_GREEN}${nextflow.version}${ANSI_RESET}
===========================================
"""
.stripIndent()
}
/*
========================================================================================
HELP MESSAGE
========================================================================================
*/
def helpMessage() {
log.info """
===========================================
${ANSI_GREEN}Sample sheet generator for various pipelines${ANSI_RESET}
This pipeline generates the samplesheets for the various options to perform a bacterial assembly.
You can choose between the three different assembly types short, long and hybrid as well as between
the two different assembly pipelines ${ANSI_GREEN}nf-core/bacass and unicycler${ANSI_RESET}.
If long reads are specified a concatination of the individual FastQ files in the barcodeX directories will be performed.
As extension the samplesheet for the ${ANSI_GREEN}imgag/plasmIDent and nf-core/viralrecon${ANSI_RESET} pipeline can be generated.
General parameters:
-------------------------------------------
--pipeline : Pipeline for which a samplesheet should be generated | bacass (default), viralrecon, unicycler or plasmident
--reads : Choice between short (default), long or hybrid assembly
--mapping_file : tab-separated mapping file, has to contain the sample IDs for short reads and sample barcodes for long reads
${ANSI_RED}has to be stored in the directory, where the pipeline is executed${ANSI_RESET}
If you want to perform a hybrid assembly the first column has to contain the sample IDs and the second the long read barcodes
--outdir : The output directory were the results will be saved
--multiqc_config : Path to multiqc configuration file, ${ANSI_RED}currently not used${ANSI_RESET}
Illumina options:
-------------------------------------------
--int_reads_input : Path to the Illumina read directory, must contain the same name as the sample IDs in the mapping file
Nanopore options:
-------------------------------------------
--ont_reads_input : Path to the nanopore directories for the individual barcodes, these will be concatinated and used for the assembly.
must contain the same name as the barcodes in the mapping file
--ont_reads_outdir : The output directory for the concatinated and renamed FastQ files for each individual barcode
Nf-core/bacass and viralrecon options:
-------------------------------------------
--samplesheet_header : comma-separated string with the header information of the samplesheets. Default is the bacass header
--genomesize : Expected genomesize in Megabases. Only used by the canu assembler in the nf-core/bacass pipeline. Default: 0
plasmIDent options:
-------------------------------------------
--plas_assemblies : The assembly directory. If no directory is given the pipeline will search for directories with the specified sample ID
--plas_outdir : The output directory for the plasmIDent pipeline, ${ANSI_RED}currently not used${ANSI_RESET}
===========================================
"""
.stripIndent()
}
/*
========================================================================================
PROCESS FINISHED MESSAGE
========================================================================================
*/
//=============================
workflow.onComplete {
if (workflow.success) {
log.info """
===========================================
${ANSI_GREEN}Finished in ${workflow.duration}
The samplesheet is here ==> ${ANSI_RESET}$params.outdir/samplesheet_${params.pipeline}.csv
===========================================
"""
.stripIndent()
}
else {
log.info """
===========================================
${ANSI_RED}Finished with errors!${ANSI_RESET}
"""
.stripIndent()
}
}