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nextflow.config
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nextflow.config
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/*
Parameters
*/
manifest {
version = '1.0'
}
// general parameters
params.split_fastq_by = 1000000
params.speed = false
params.output = "./output/" //PATH leading to directory in which output is supposed to be stored
params.mapq = 2 //INT minimum mapq-score needed to retain an alignment -> soon to be deprecated
//non essential input files
params.annotation = 'NO_FILE'
// Parameters for preprocessing
params.min_length = 30 //INT minimum length of reads required after preprocessing
params.min_qual = 20 //INT minimum quality of nucleotide required to retain it
params.min_percent_qual_filter = 90 //INT minimum percentage of nucleotides in a read required to have their quality above params.min_qual to retain the read
// Parameters for barcode handling
params.barcode_pattern = "NNNNNXXXXXXNNNN" //STRING containing barcode pattern -> N = random barcode; X = experimental barcode
params.barcode_mismatches = 1 //INT maximum number of mismatches in the experimental barcode sequence to still allocate the read
// Parameters for alignment
params.domain = "pro" //STRING decides if bowtie2 or STAR is used -> pro = bowtie2; eu = STAR
params.max_alignments = false
params.report_all_alignments = false
// Parameters for replicate merging
params.merge_replicates = false
params.correlation_analysis = false
params.combine_strands_correlation = false
// Parameters for transcript analysis
params.map_to_transcripts = false //BOOLEAN decides if top X sequences from the reference are presented in the output
params.number_top_transcripts = 10 //INT number of top transcripts presented when params.map_to_transcripts = true
// Parameters for peak calling
params.omit_peak_calling = false //BOOLEAN decides if peak calling via pureclip takes place after normal processing
params.peak_calling_for_high_coverage = false //BOOLEAN adds arguments to PureCLIP which allow the tool to run with BAM files containing coverages all over the reference
params.peak_calling_regions = false
params.peak_calling_regions_width = 8
// Parameters for RNA subtype distribution
params.gene_id = "ID" //STRING name of gene_id used within the annotation file
params.color_barplot = "#69b3a2" //STRING color used for barplots
//params.rna_subtypes = 'lnc_RNA,miRNA,mRNA,ncRNA,rRNA,snoRNA,snRNA,tRNA'
params.rna_subtypes = '3_prime_UTR,transcript,5_prime_UTR' //STRING RNA-subtypes used for the distribution of CL-sites
// Parameters for peak distance analysis
params.omit_peak_distance = false
params.percentile = 90 //INT percentile that decides which cl-sites are considered when calculating distances and extracting sequences
params.distance = 30 //INT maximum distance to check for distances between cl-sites
// Parameters for sequence extraction and motif search
params.omit_sequence_extraction = false
params.seq_len = 20 //INT length to both sides of cl-sites from which nucleotides are recovered
params.omit_cl_nucleotide = false
params.omit_cl_width = 0 // INT number of nucleotides to be replaced with ends on both sides of the cl-site
params.remove_overlaps = false // BOOL
params.max_motif_num = 50 // INT max number of motifs to search for
params.min_motif_width = 8 // INT minimum motif width to report, >=3
params.max_motif_width = 15 // INT maximum motif width to report, <= 30
/*
Parameters end
*/
profiles {
sge {
process.executor = 'sge'
process.shell = ['/usr/bin/env', 'bash']
process.queue = 'all.q'
process.clusterOptions = '-V -S /bin/bash'
process.penv = 'multislot'
}
slurm {
process.executor = 'slurm'
}
local {
process.executor = 'local'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
docker {
docker.enabled = true
runOptions = '-u $(id -u):$(id -g)'
}
podman {
podman.enabled = true
}
}
process {
withName: 'quality_control|quality_control_2' {
cpus = 1
memory = '1 GB'
container = 'docker:https://pbarth/fastqc:1.0'
}
withName: adapter_removal {
cpus = 1
memory = '5 GB'
container = 'docker:https://pbarth/trim_galore:1.0'
}
withName: quality_filter {
cpus = 1
memory = '1 GB'
container = 'docker:https://pbarth/fastx:1.0'
}
withName: remove_exp_barcode {
cpus = 1
memory = '100 MB'
container = 'docker:https://pbarth/fastx:1.0'
}
withName: extract_rnd_barcode {
cpus = 1
memory = '1 GB'
container = 'docker:https://pbarth/umi-tools:1.0'
}
withName: deduplicate {
cpus = 1
//memory = '100 GB'
container = 'docker:https://pbarth/umi-tools:1.0'
}
withName: check_barcode_file{
cpus = 1
memory = '200 MB'
container = 'docker:https://pbarth/checkbarcode:1.0'
}
withName: 'get_length_exp_barcode|merge_preprocessed_reads|get_top_hits|remove_newlines|extract_top_transcript_sequences|collect_experiments_without_alignments|collect_subtype_analysis_errors|collect_workflow_metrics' {
cpus = 1
memory = '500 MB'
container = 'docker:https://pbarth/base:1.0'
}
withName: 'merge_deduplicated_bam|count_hits|filter_empty_bams|sort_bam|sort_bam_before_strand_pref|determine_strand_preference|index_alignments|extract_top_alignments|index_for_peak_calling|sort_and_index_alignment|get_chromosome_sizes' {
cpus = 1
memory = '10 GB'
container = 'docker:https://pbarth/samtools:1.0'
}
withName: 'split_bam_by_chromosome' {
cpus = 1
memory = '500 MB'
container = 'docker:https://pbarth/bamtools:1.0'
}
withName: 'merge_wigs' {
cpus = 1
memory = '20 GB'
container = 'docker:https://pbarth/merge:1.0.1'
}
withName: 'wig_to_bigWig|bigWig_to_bedgraph' {
cpus = 1
memory = '500 MB'
container = 'docker:https://pbarth/wigtobigwig:1.0'
}
withName: split_exp_barcode {
cpus = 1
memory = '500 MB'
container = 'docker:https://pbarth/fastx:1.0'
}
withName: 'build_index_bowtie|mapping_bowtie' {
cpus = 4
memory = '5 GB'
container = 'docker:https://pbarth/bowtie2:1.0'
}
withName: 'build_index_STAR|mapping_STAR' {
cpus = 8
memory = '100 GB'
container = 'docker:https://pbarth/star:1.0'
}
withName: 'calculate_crosslink_sites|split_wig_2_for_peak_height_hist|split_wig2_for_correlation' {
cpus = 1
memory = '10 GB'
container = 'docker:https://pbarth/determine_cl_sites:1.0'
}
withName: feature_counts {
cpus = 1
memory = '1 GB'
container = 'docker:https://pbarth/subread:1.0'
}
withName: pureCLIP {
cpus = 8
memory = '50 GB'
container = 'quay.io/biocontainers/pureclip:1.3.1--0'
}
withName: pureCLIP_to_wig {
cpus = 1
memory = '1 GB'
container = 'docker:https://pbarth/wig-to-wig2:1.0'
}
withName: multiqc {
cpus = 1
memory = '10 GB'
container = 'docker:https://pbarth/multiqc:1.0'
}
withName: wig_to_bam {
cpus = 1
memory = '10 GB'
container = 'docker:https://pbarth/wig2bam:1.0'
}
withName: get_RNA_subtypes_distribution{
cpus = 1
memory = '10 GB'
container = 'docker:https://pbarth/rna_subtypes_distribution:1.0.1'
}
withName: 'generate_RNA_subtypes_barplot|plot_peak_distance|generate_barcode_barplot|visualize_strand_preference|generate_peak_height_histogram' {
cpus = 1
memory = '5 GB'
container = 'docker:https://pbarth/rplots:1.0.3'
}
withName: 'calc_wig_correlation' {
cpus = 1
memory = '10 GB'
container = 'docker:https://pbarth/rplots:1.0.3'
}
withName: sequence_extraction{
cpus = 1
memory = '500 MB'
container = 'docker:https://pbarth/sequence_extraction:1.0.1'
}
withName: prepare_annotation_for_igv {
cpus = 1
memory = '5 GB'
container = 'docker:https://pbarth/igvprep:1.0'
}
withName: generate_igv_session {
cpus = 1
memory = '1 GB'
container = 'docker:https://pbarth/igvsession:1.0'
}
withName: motif_search{
cpus = 1
memory = '5 GB'
container = 'docker:https://pbarth/meme:1.0'
}
withName: calculate_peak_distance{
cpus = 1
memory = '2 GB'
container = 'docker:https://pbarth/peak_distance:1.0'
}
}