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peaseq-case.wdl
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peaseq-case.wdl
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version 1.0
import "workflows/tasks/fastqc.wdl"
import "workflows/tasks/bedtools.wdl"
import "workflows/tasks/bowtie.wdl"
import "workflows/tasks/samtools.wdl"
import "workflows/tasks/macs.wdl"
import "workflows/workflows/bamtogff.wdl"
import "workflows/tasks/sicer.wdl"
import "workflows/workflows/motifs.wdl"
import "workflows/tasks/rose.wdl"
import "workflows/tasks/seaseq_util.wdl" as util
import "workflows/workflows/visualization.wdl" as viz
import "workflows/workflows/mapping.wdl"
import "workflows/tasks/runspp.wdl"
import "workflows/tasks/sortbed.wdl"
import "workflows/tasks/sratoolkit.wdl" as sra
import "workflows/tasks/peaseq_util.wdl"
workflow peaseq {
String pipeline_ver = 'v1.0.0'
meta {
title: 'PEAseq Analysis'
summary: 'Paired-End Antibody Sequencing (PEAseq) Pipeline'
description: 'A comprehensive automated computational pipeline for all ChIP-Seq/CUT&RUN data analysis.'
version: '1.0.0'
details: {
citation: 'https://doi.org/10.1186/s12859-022-04588-z',
contactEmail: '[email protected]',
contactOrg: "St Jude Children's Research Hospital",
contactUrl: "",
upstreamLicenses: "MIT",
upstreamUrl: 'https://github.com/stjude/seaseq',
whatsNew: [
{
version: "1.0",
changes: ["Initial release"]
}
]
}
parameter_group: {
reference_genome: {
title: 'Reference genome',
description: 'Genome specific files. e.g. reference FASTA, GTF, blacklist, motif databases, FASTA index, bowtie index .',
help: 'Input reference genome files as defined. If some genome data are missing then analyses using such data will be skipped.'
},
input_genomic_data: {
title: 'Input FASTQ data',
description: 'Genomic input files for experiment.',
help: 'Input one or more sample data and/or SRA identifiers.'
},
analysis_parameter: {
title: 'Analysis parameter',
description: 'Analysis settings needed for experiment.',
help: 'Analysis settings; such output analysis file name.'
}
}
}
input {
# group: reference_genome
File reference
File? spikein_reference
File? blacklist
File gtf
Array[File]? bowtie_index
Array[File]? spikein_bowtie_index
Array[File]? motif_databases
# group: input_genomic_data
Array[String]? sample_sraid
Array[File]? sample_R1_fastq
Array[File]? sample_R2_fastq
# group: analysis_parameter
# Read Mapping parameters for bowtie
Int? insertsize = 600
String? strandedness = "fr"
# Additional options
String? results_name
Boolean run_motifs=true
}
parameter_meta {
reference: {
description: 'Reference FASTA file',
group: 'reference_genome',
patterns: ["*.fa", "*.fasta", "*.fa.gz", "*.fasta.gz"]
}
blacklist: {
description: 'Blacklist file in BED format',
group: 'reference_genome',
help: 'If defined, blacklist regions listed are excluded after reference alignment.',
patterns: ["*.bed", "*.bed.gz"]
}
gtf: {
description: 'gene annotation file (.gtf)',
group: 'reference_genome',
help: 'Input gene annotation file from RefSeq or GENCODE (.gtf).',
patterns: ["*.gtf", "*.gtf.gz", "*.gff", "*.gff.gz", "*.gff3", "*.gff3.gz"]
}
bowtie_index: {
description: 'bowtie v1 index files (*.ebwt)',
group: 'reference_genome',
help: 'If not defined, bowtie v1 index files are generated, will take a longer compute time.',
patterns: ["*.ebwt"]
}
motif_databases: {
description: 'One or more of the MEME suite motif databases (*.meme)',
group: 'reference_genome',
help: 'Input one or more motif databases available from the MEME suite (https://meme-suite.org/meme/db/motifs).',
patterns: ["*.meme"]
}
sample_sraid: {
description: 'One or more sample SRA (Sequence Read Archive) run identifiers',
group: 'input_genomic_data',
help: 'Input publicly available FASTQs (SRRs). Multiple SRRs are separated by commas (,).',
example: 'SRR12345678'
}
sample_R1_fastq: {
description: 'One or more sample R1 FASTQs',
group: 'input_genomic_data',
help: 'Upload zipped FASTQ files.',
patterns: ["*.fq.gz", "*.fastq.gz"]
}
sample_R2_fastq: {
description: 'One or more sample R2 FASTQs',
group: 'input_genomic_data',
help: 'Upload zipped FASTQ files.',
patterns: ["*.fq.gz", "*.fastq.gz"]
}
results_name: {
description: 'Experiment results custom name',
group: 'analysis_parameter',
help: 'Input preferred analysis results name (recommended if multiple FASTQs are provided).',
example: 'AllMerge_mapped'
}
run_motifs: {
description: 'Perform Motif Analysis',
group: 'analysis_parameter',
help: 'Setting this means Motif Discovery and Enrichment analysis will be performed.',
example: true
}
insertsize: {
description: 'Bowtie v1 maximum insert size (-X/--maxins <int>).',
group: 'analysis_parameter',
help: 'Specify maximum insert size for paired-end alignment (default: 600).',
example: 600
}
strandedness: {
description: 'Bowtie v1 mate orientation (--fr/--rf/--ff).',
group: 'analysis_parameter',
help: 'The upstream/downstream mate orientation for paired-end alignment (default: --fr).',
example: 'fr'
}
}
### ------------------------------------------------- ###
### ---------------- S E C T I O N 1 ---------------- ###
### ----------- Pre-process Analysis Files ---------- ###
### ------------------------------------------------- ###
# Process SRRs
if ( defined(sample_sraid) ) {
# Download sample file(s) from SRA database
# outputs:
# fastqdump.fastqfile : downloaded sample files in fastq.gz format
Array[String] string_sra = [1] #buffer to allow for sra_id optionality
Array[String] s_sraid = select_first([sample_sraid, string_sra])
scatter (eachsra in s_sraid) {
call sra.fastqdump {
input :
sra_id=eachsra,
cloud=false
}
File R1end = select_first([fastqdump.R1end, string_sra[0]])
File R2end = select_first([fastqdump.R2end, string_sra[0]])
} # end scatter each sra
Array[File] sample_R1_srafile = R1end
Array[File] sample_R2_srafile = R2end
} # end if sample_sraid
# Generating INDEX files
#1. Bowtie INDEX files if not provided
if ( !defined(bowtie_index) ) {
# create bowtie index when not provided
call bowtie.index as bowtie_idx {
input :
reference=reference
}
}
#2. Make sure indexes are six else build indexes
if ( defined(bowtie_index) ) {
# check total number of bowtie indexes provided
Array[String] string_bowtie_index = [1] #buffer to allow for bowtie_index optionality
Array[File] int_bowtie_index = select_first([bowtie_index, string_bowtie_index])
if ( length(int_bowtie_index) != 6 ) {
# create bowtie index if 6 index files aren't provided
call bowtie.index as bowtie_idx_2 {
input :
reference=reference
}
}
}
Array[File] actual_bowtie_index = select_first([bowtie_idx_2.bowtie_indexes, bowtie_idx.bowtie_indexes, bowtie_index])
# Spike-in DNA
#3. Bowtie INDEX files if not provided
String string_spikein = "1"
Array[String] string_spikein_buffer = [1]
if ( !defined(spikein_bowtie_index) && defined(spikein_reference) ) {
# create bowtie index on spikein genome
call bowtie.index as spikein_bowtie_idx {
input :
reference=select_first([spikein_reference, string_spikein])
}
}
#4. Make sure indexes are six else build indexes for Spike-in DNA
if ( defined(spikein_bowtie_index) ) {
# check total number of bowtie indexes provided
Array[File] int_spikein_bowtie_index = select_first([spikein_bowtie_index, string_spikein_buffer])
if ( length(int_spikein_bowtie_index) != 6 ) {
# create bowtie index if 6 index files aren't provided
call bowtie.index as spikein_bowtie_idx_2 {
input :
reference=select_first([spikein_reference, string_spikein])
}
}
}
Array[File] actual_spikein_bowtie_index = select_first([spikein_bowtie_idx_2.bowtie_indexes, spikein_bowtie_idx.bowtie_indexes, spikein_bowtie_index, string_spikein_buffer])
# FASTA faidx and chromsizes and effective genome size
call samtools.faidx as samtools_faidx {
# create FASTA index and chrom sizes files
input :
reference=reference
}
call util.effective_genome_size as egs {
# effective genome size for FASTA
input :
reference=reference
}
# Process FASTQs
if ( defined(sample_R1_fastq) ) {
Array[String] string_fastq = [1] #buffer to allow for fastq optionality
Array[File] s_R1_fastq = select_first([sample_R1_fastq, string_fastq])
Array[File] sample_R1_fastqfile = s_R1_fastq
Array[File] s_R2_fastq = select_first([sample_R2_fastq, string_fastq])
Array[File] sample_R2_fastqfile = s_R2_fastq
# Order FASTQs
if (length(sample_R1_fastqfile) > 1) {
call peaseq_util.sortfiles as R1_sorted { input: fastqfiles=sample_R1_fastqfile }
call peaseq_util.sortfiles as R2_sorted { input: fastqfiles=sample_R2_fastqfile }
}
Array[File] sample_R1_fastqfiles = select_first([R1_sorted.allfiles, sample_R1_fastqfile])
Array[File] sample_R2_fastqfiles = select_first([R2_sorted.allfiles, sample_R2_fastqfile])
}
# collate all fastqfiles
Array[File] original_sample_R1 = flatten(select_all([sample_R1_srafile, sample_R1_fastqfiles]))
Array[File] original_sample_R2 = flatten(select_all([sample_R2_srafile, sample_R2_fastqfiles]))
Array[File] original_all_sample_fastqfiles = flatten(select_all([sample_R1_srafile, sample_R1_fastqfiles,sample_R2_srafile, sample_R2_fastqfiles]))
# transpose to paired-end tuples
Array[Pair[File, File]] original_sample_fastqfiles = zip(original_sample_R1, original_sample_R2)
### ------------------------------------------------- ###
### ---------------- S E C T I O N 1 ---------------- ###
### ----------- B: remove Spike-IN reads ------------ ###
### ------------------------------------------------- ###
# if multiple fastqfiles are provided
Boolean multi_fastqpair = if length(original_sample_fastqfiles) > 1 then true else false
Boolean one_fastqpair = if length(original_sample_fastqfiles) == 1 then true else false
if ( defined(spikein_bowtie_index) || defined(spikein_reference) ) {
scatter (eachfastq in original_all_sample_fastqfiles) {
call fastqc.fastqc as spikein_indv_fastqc {
input :
inputfile=eachfastq,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/FastQC' else if defined(results_name) then results_name + '/SpikeIn/FastQC' else sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/FastQC'
}
}
scatter (fastqpair in original_sample_fastqfiles) {
call util.basicfastqstats as spikein_indv_R1_bfs {
input :
fastqfile=fastqpair.left,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats' else if defined(results_name) then results_name + '/SpikeIn/SummaryStats' else sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats'
}
call bowtie.spikein_PE as spikein_indv_map {
input :
fastqfile=fastqpair.left,
fastqfile_R2=fastqpair.right,
metricsfile=spikein_indv_R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_spikein_bowtie_index,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats' else if defined(results_name) then results_name + '/SpikeIn/SummaryStats' else sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats'
}
}
if (length(original_sample_R1) > 1) {
call peaseq_util.sortfiles as spikein_R1_sorted { input: fastqfiles=spikein_indv_map.unaligned_1 }
call peaseq_util.sortfiles as spikein_R2_sorted { input: fastqfiles=spikein_indv_map.unaligned_2 }
}
Array[File] spikein_sample_R1 = select_first([spikein_R1_sorted.allfiles, spikein_indv_map.unaligned_1])
Array[File] spikein_sample_R2 = select_first([spikein_R2_sorted.allfiles, spikein_indv_map.unaligned_2])
Array[File] spikein_all_sample_fastqfiles = flatten(select_all([spikein_sample_R1, spikein_sample_R2]))
Array[Pair[File, File]] spikein_sample_fastqfiles = zip(spikein_sample_R1, spikein_sample_R2)
}
Array[File] all_sample_fastqfiles = select_first([spikein_all_sample_fastqfiles, original_all_sample_fastqfiles])
Array[Pair[File, File]] sample_fastqfiles = select_first([spikein_sample_fastqfiles, original_sample_fastqfiles])
### ------------------------------------------------- ###
### ---------------- S E C T I O N 2 ---------------- ###
### ---- Single End (SE) Mode for all fastqfiles ---- ###
### ------------------------------------------------- ###
scatter (eachfastq in all_sample_fastqfiles) {
call fastqc.fastqc as indv_fastqc {
input :
inputfile=eachfastq,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else if defined(results_name) then results_name + '/single-end_mode/QC/FastQC' else sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/FastQC'
}
call util.basicfastqstats as indv_bfs {
input :
fastqfile=eachfastq,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else if defined(results_name) then results_name + '/single-end_mode/QC/SummaryStats' else sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/SummaryStats'
}
call mapping.mapping as indv_mapping {
input :
fastqfile=eachfastq,
index_files=actual_bowtie_index,
metricsfile=indv_bfs.metrics_out,
blacklist=blacklist,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files' else if defined(results_name) then results_name + '/single-end_mode/BAM_files' else sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
call fastqc.fastqc as indv_bamfqc {
input :
inputfile=indv_mapping.sorted_bam,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else if defined(results_name) then results_name + '/single-end_mode/QC/FastQC' else sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/FastQC'
}
call runspp.runspp as indv_runspp {
input:
bamfile=select_first([indv_mapping.bklist_bam, indv_mapping.sorted_bam])
}
call bedtools.bamtobed as indv_bamtobed {
input:
bamfile=select_first([indv_mapping.bklist_bam, indv_mapping.sorted_bam])
}
call util.evalstats as indv_summarystats {
input:
fastq_type="PEAseq Sample FASTQ",
bambed=indv_bamtobed.bedfile,
sppfile=indv_runspp.spp_out,
fastqczip=indv_fastqc.zipfile,
bamflag=indv_mapping.bam_stats,
rmdupflag=indv_mapping.mkdup_stats,
bkflag=indv_mapping.bklist_stats,
fastqmetrics=indv_bfs.metrics_out,
default_location=if multi_fastqpair then 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else if defined(results_name) then results_name + '/single-end_mode/QC/SummaryStats' else sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/SummaryStats'
}
} # end scatter (for eachfastq)
# MERGE BAM files
# Execute analysis on merge bam file
# Analysis executed:
# Merge BAM (SE mode : for each fastq paired-end)
call util.mergehtml {
input:
htmlfiles=indv_summarystats.xhtml,
txtfiles=indv_summarystats.textfile,
default_location='SAMPLE',
outputfile = 'AllSamples-summary-stats.html'
}
call samtools.mergebam as SE_mergebam {
input:
bamfiles=indv_mapping.sorted_bam,
metricsfiles=indv_bfs.metrics_out,
default_location = if defined(results_name) then results_name + '/single-end_mode/BAM_files' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files',
outputfile = 'AllMapped_' + length(all_sample_fastqfiles) + 'fastqs_SE.sorted.bam'
}
call fastqc.fastqc as SE_mergebamfqc {
input:
inputfile=SE_mergebam.mergebam,
default_location=if defined(results_name) then results_name + '/single-end_mode/QC/FastQC' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/QC/FastQC' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/FastQC'
}
call samtools.indexstats as SE_mergeindexstats {
input:
bamfile=SE_mergebam.mergebam,
default_location=if defined(results_name) then results_name + '/single-end_mode/BAM_files' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
if ( defined(blacklist) ) {
# remove blacklist regions
String string_blacklist = "" #buffer to allow for blacklist optionality
File blacklist_file = select_first([blacklist, string_blacklist])
call bedtools.intersect as SE_merge_rmblklist {
input :
fileA=SE_mergebam.mergebam,
fileB=blacklist_file,
default_location=if defined(results_name) then results_name + '/single-end_mode/BAM_files' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files',
nooverlap=true
}
call samtools.indexstats as SE_merge_bklist {
input :
bamfile=SE_merge_rmblklist.intersect_out,
default_location=if defined(results_name) then results_name + '/single-end_mode/BAM_files' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
} # end if blacklist provided
File SE_mergebam_afterbklist = select_first([SE_merge_rmblklist.intersect_out, SE_mergebam.mergebam])
call samtools.markdup as SE_merge_markdup {
input :
bamfile=SE_mergebam_afterbklist,
default_location=if defined(results_name) then results_name + '/single-end_mode/BAM_files' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
call samtools.indexstats as SE_merge_mkdup {
input :
bamfile=SE_merge_markdup.mkdupbam,
default_location=if defined(results_name) then results_name + '/single-end_mode/BAM_files' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
### ------------------------------------------------- ###
### ---------------- S E C T I O N 3 ---------------- ###
### ---- Paired End (PE) Mode for all fastqfiles ---- ###
### ---- A: analysis if multiple FASTQs provided ---- ###
### ------------------------------------------------- ###
if ( multi_fastqpair ) {
scatter (fastqpair in sample_fastqfiles) {
# Execute analysis on each fastq file provided
# Analysis executed:
# Reference Alignment using Bowtie (-k2 -m2)
# Convert SAM to BAM
# FastQC on BAM files
# Remove Blacklists (if provided)
# Remove read duplicates
# Summary statistics on FASTQs
# Combine html files into one for easy viewing
call util.basicfastqstats as indv_R1_bfs {
input :
fastqfile=fastqpair.left,
default_location='SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
call mapping.mapping as indv_PE_mapping {
input :
fastqfile=fastqpair.left,
fastqfile_R2=fastqpair.right,
metricsfile=indv_R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_bowtie_index,
blacklist=blacklist,
paired_end=true,
default_location='SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files'
}
call fastqc.fastqc as indv_PE_bamfqc {
input :
inputfile=indv_PE_mapping.sorted_bam,
default_location='SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call runspp.runspp as indv_PE_runspp {
input:
bamfile=select_first([indv_PE_mapping.bklist_bam, indv_PE_mapping.sorted_bam])
}
call peaseq_util.pe_bamtobed as indv_PE_bamtobed {
input:
bamfile=select_first([indv_PE_mapping.bklist_bam, indv_PE_mapping.sorted_bam])
}
call util.evalstats as indv_PE_summarystats {
input:
fastq_type="PEAseq Sample FASTQ",
bambed=indv_PE_bamtobed.bedfile,
sppfile=indv_PE_runspp.spp_out,
fastqczip=indv_PE_bamfqc.zipfile,
bamflag=indv_PE_mapping.bam_stats,
rmdupflag=indv_PE_mapping.mkdup_stats,
bkflag=indv_PE_mapping.bklist_stats,
default_location='SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
} # end scatter (for each sample fastq)
# MERGE BAM FILES
# Execute analysis on merge bam file
# Analysis executed:
# Merge BAM (if more than 1 fastq is provided)
# FastQC on Merge BAM (AllMapped_<number>_mapped)
# merge bam files and perform fasTQC if more than one is provided
call util.mergehtml as PE_mergehtml {
input:
htmlfiles=indv_PE_summarystats.xhtml,
txtfiles=indv_PE_summarystats.textfile,
default_location='SAMPLE',
outputfile = 'AllMapped_PEmode_peaseq-summary-stats.html'
}
call peaseq_util.pe_mergehtml as final_mergehtml {
input:
pe_htmlfiles=indv_PE_summarystats.xhtml,
pe_txtfiles=indv_PE_summarystats.textfile,
se_htmlfiles=indv_summarystats.xhtml,
se_txtfiles=indv_summarystats.textfile,
default_location='SAMPLE',
outputfile = 'AllSamples-summary-stats.html'
}
call samtools.mergebam as PE_mergebam {
input:
bamfiles=indv_PE_mapping.as_sortedbam,
metricsfiles=indv_bfs.metrics_out,
paired_end=true,
default_location = if defined(results_name) then results_name + '/BAM_files' else 'AllMapped_' + length(indv_PE_mapping.sorted_bam) + 'fastqpairs/BAM_files',
outputfile = if defined(results_name) then results_name + '.sorted.bam' else 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs.sorted.bam',
fixmatefile = if defined(results_name) then results_name + '.fixmate.bam' else 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs.fixmate.bam'
}
call fastqc.fastqc as PE_mergebamfqc {
input:
inputfile=PE_mergebam.mergebam,
default_location=sub(basename(PE_mergebam.mergebam),'.sorted.b.*$','') + '/QC/FastQC'
}
call samtools.indexstats as PE_mergeindexstats {
input:
bamfile=PE_mergebam.mergebam,
default_location=sub(basename(PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
if ( defined(blacklist) ) {
# remove blacklist regions
String string_pe_blacklist = "" #buffer to allow for blacklist optionality
File blacklist_pe = select_first([blacklist, string_pe_blacklist])
String string_pe_fixmate = "" #buffer to allow for blacklist optionality
File fixmate_pe = select_first([PE_mergebam.fixmatemergebam, string_pe_fixmate])
call bedtools.pairtobed as PE_merge_rmblklist {
input :
fileA=fixmate_pe,
fileB=blacklist_pe,
default_location=sub(basename(PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
call samtools.indexstats as PE_merge_bklist {
input :
bamfile=PE_merge_rmblklist.pairtobed_out,
default_location=sub(basename(PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
} # end if blacklist provided
File PE_mergebam_afterbklist = select_first([PE_merge_rmblklist.pairtobed_out, PE_mergebam.mergebam])
call samtools.markdup as PE_merge_markdup {
input :
bamfile=PE_mergebam_afterbklist,
default_location=sub(basename(PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
call samtools.indexstats as PE_merge_mkdup {
input :
bamfile=PE_merge_markdup.mkdupbam,
default_location=sub(basename(PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
} # end if length(fastqfiles) > 1: multi_fastqpair
### ------------------------------------------------- ###
### ---------------- S E C T I O N 3 ---------------- ###
### ---- Paired End (PE) Mode for all fastqfiles ---- ###
### ------- B: analysis if one FASTQ provided ------- ###
### ------------------------------------------------- ###
# if only one fastqfile is provided
if ( one_fastqpair ) {
# Execute analysis on each fastq file provided
# Analysis executed:
# FastQC
# FASTQ read length distribution
# Reference Alignment using Bowtie (-k2 -m2)
# Convert SAM to BAM
# FastQC on BAM files
# Remove Blacklists (if provided)
# Remove read duplicates
# Summary statistics on FASTQs
# Combine html files into one for easy viewing
call util.basicfastqstats as R1_bfs {
input :
fastqfile=sample_fastqfiles[0].left,
default_location=if defined(results_name) then results_name + '/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
call mapping.mapping as uno_PE_mapping {
input :
fastqfile=sample_fastqfiles[0].left,
fastqfile_R2=sample_fastqfiles[0].right,
metricsfile=R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_bowtie_index,
blacklist=blacklist,
paired_end=true,
results_name=results_name,
default_location=if defined(results_name) then results_name + '/BAM_files' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files'
}
call fastqc.fastqc as uno_PE_bamfqc {
input :
inputfile=uno_PE_mapping.sorted_bam,
default_location=sub(basename(uno_PE_mapping.sorted_bam),'.sorted.bam','') + '/QC/FastQC'
}
call runspp.runspp as uno_PE_runspp {
input:
bamfile=select_first([uno_PE_mapping.bklist_bam, uno_PE_mapping.sorted_bam])
}
call peaseq_util.pe_bamtobed as uno_PE_bamtobed {
input:
bamfile=select_first([uno_PE_mapping.bklist_bam, uno_PE_mapping.sorted_bam])
}
} # end if length(fastqfiles) == 1: one_fastqpair
### ------------------------------------------------- ###
### ---------------- S E C T I O N 4 ---------------- ###
### --------------- ChIP-seq Analysis --------------- ###
### ------------ A: analysis for SE mode ----------- ###
### ------------------------------------------------- ###
# ChIP-seq and downstream analysis
# Execute analysis on merge bam file
# Analysis executed:
# Peaks identification (SICER, MACS, ROSE)
# Motif analysis
call macs.macs as SE_macs {
input :
bamfile=SE_mergebam_afterbklist,
pvalue="1e-9",
keep_dup="auto",
egs=egs.genomesize,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-p9_kd-auto' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-p9_kd-auto' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-p9_kd-auto',
coverage_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_p9_kd-auto' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_p9_kd-auto' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_p9_kd-auto'
}
call util.addreadme as SE_addreadme {
input :
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS'
}
call macs.macs as SE_all {
input :
bamfile=SE_mergebam_afterbklist,
pvalue="1e-9",
keep_dup="all",
egs=egs.genomesize,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-p9_kd-all' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-p9_kd-all' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-p9_kd-all',
coverage_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_p9_kd-all' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_p9_kd-all' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_p9_kd-all'
}
call macs.macs as SE_nomodel {
input :
bamfile=SE_mergebam_afterbklist,
nomodel=true,
egs=egs.genomesize,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-nm' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-nm' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '-nm',
coverage_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_nm' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_nm' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + basename(SE_mergebam_afterbklist,'.bam') + '_nm'
}
call bamtogff.bamtogff as SE_bamtogff {
input :
gtffile=gtf,
chromsizes=samtools_faidx.chromsizes,
bamfile=SE_merge_markdup.mkdupbam,
bamindex=SE_merge_mkdup.indexbam,
default_location = if defined(results_name) then results_name + '/single-end_mode/BAM_Density' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/BAM_Density' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_Density'
}
call bedtools.bamtobed as SE_forsicerbed {
input :
bamfile=SE_merge_markdup.mkdupbam
}
call sicer.sicer as SE_sicer {
input :
bedfile=SE_forsicerbed.bedfile,
chromsizes=samtools_faidx.chromsizes,
genome_fraction=egs.genomefraction,
fragmentlength=SE_mergebam.avg_readlength,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS/BROAD_peaks' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS/BROAD_peaks' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS/BROAD_peaks',
coverage_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/BROAD_peaks' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/BROAD_peaks' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/BROAD_peaks'
}
call rose.rose as SE_rose {
input :
gtffile=gtf,
bamfile=SE_merge_markdup.mkdupbam,
bamindex=SE_merge_mkdup.indexbam,
bedfile_auto=SE_macs.peakbedfile,
bedfile_all=SE_all.peakbedfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS/STITCHED_peaks' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS/STITCHED_peaks' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS/STITCHED_peaks'
}
call runspp.runspp as SE_runspp {
input:
bamfile=SE_mergebam_afterbklist
}
call util.peaksanno as SE_peaksanno {
input :
gtffile=gtf,
bedfile=SE_macs.peakbedfile,
chromsizes=samtools_faidx.chromsizes,
summitfile=SE_macs.summitsfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_macs.peakbedfile),'_peaks.bed','') else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_macs.peakbedfile),'_peaks.bed','') else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_macs.peakbedfile),'_peaks.bed','')
}
call util.peaksanno as SE_all_peaksanno {
input :
gtffile=gtf,
bedfile=SE_all.peakbedfile,
chromsizes=samtools_faidx.chromsizes,
summitfile=SE_all.summitsfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_all.peakbedfile),'_peaks.bed','') else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_all.peakbedfile),'_peaks.bed','') else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_all.peakbedfile),'_peaks.bed','')
}
call util.peaksanno as SE_nomodel_peaksanno {
input :
gtffile=gtf,
bedfile=SE_nomodel.peakbedfile,
chromsizes=samtools_faidx.chromsizes,
summitfile=SE_nomodel.summitsfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_nomodel.peakbedfile),'_peaks.bed','') else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_nomodel.peakbedfile),'_peaks.bed','') else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(SE_nomodel.peakbedfile),'_peaks.bed','')
}
call util.peaksanno as SE_sicer_peaksanno {
input :
gtffile=gtf,
bedfile=SE_sicer.scoreisland,
chromsizes=samtools_faidx.chromsizes,
default_location = if defined(results_name) then results_name + '/single-end_mode/PEAKS_Annotation/BROAD_peaks' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/PEAKS_Annotation/BROAD_peaks' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/PEAKS_Annotation/BROAD_peaks'
}
# Motif Analysis
if (run_motifs) {
call motifs.motifs as SE_motifs {
input:
reference=reference,
reference_index=samtools_faidx.faidx_file,
bedfile=SE_macs.peakbedfile,
motif_databases=motif_databases,
default_location = if defined(results_name) then results_name + '/single-end_mode/MOTIFS' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/MOTIFS' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/MOTIFS'
}
call util.flankbed as SE_flankbed {
input :
bedfile=SE_macs.summitsfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/MOTIFS' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/MOTIFS' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/MOTIFS'
}
call motifs.motifs as SE_flank {
input:
reference=reference,
reference_index=samtools_faidx.faidx_file,
bedfile=SE_flankbed.flankbedfile,
motif_databases=motif_databases,
default_location = if defined(results_name) then results_name + '/single-end_mode/MOTIFS' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/MOTIFS' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/MOTIFS'
}
}
call viz.visualization as SE_visualization {
input:
wigfile=SE_macs.wigfile,
chromsizes=samtools_faidx.chromsizes,
xlsfile=SE_macs.peakxlsfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_macs.peakbedfile),'_peaks.bed','') else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_macs.peakbedfile),'_peaks.bed','') else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_macs.peakbedfile),'_peaks.bed','')
}
call viz.visualization as SE_vizall {
input:
wigfile=SE_all.wigfile,
chromsizes=samtools_faidx.chromsizes,
xlsfile=SE_all.peakxlsfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_all.peakbedfile),'_peaks.bed','') else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_all.peakbedfile),'_peaks.bed','') else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_all.peakbedfile),'_peaks.bed','')
}
call viz.visualization as SE_viznomodel {
input:
wigfile=SE_nomodel.wigfile,
chromsizes=samtools_faidx.chromsizes,
xlsfile=SE_nomodel.peakxlsfile,
default_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_nomodel.peakbedfile),'_peaks.bed','') else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_nomodel.peakbedfile),'_peaks.bed','') else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/NARROW_peaks' + '/' + sub(basename(SE_nomodel.peakbedfile),'_peaks.bed','')
}
call viz.visualization as SE_vizsicer {
input:
wigfile=SE_sicer.wigfile,
chromsizes=samtools_faidx.chromsizes,
default_location = if defined(results_name) then results_name + '/single-end_mode/COVERAGE_files/BROAD_peaks' else if multi_fastqpair then 'AllMapped_' + length(sample_fastqfiles) + 'fastqpairs' + '/single-end_mode/COVERAGE_files/BROAD_peaks' else sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/COVERAGE_files/BROAD_peaks'
}
call bedtools.bamtobed as SE_finalbed {
input:
bamfile=SE_mergebam_afterbklist
}
call sortbed.sortbed as SE_sortbed {
input:
bedfile=SE_finalbed.bedfile
}
call bedtools.intersect as SE_intersect {
input:
fileA=SE_macs.peakbedfile,
fileB=SE_sortbed.sortbed_out,
countoverlap=true,
sorted=true
}
### ------------------------------------------------- ###
### ---------------- S E C T I O N 4 ---------------- ###
### --------------- ChIP-seq Analysis --------------- ###
### ------------ B: analysis for PE mode ----------- ###
### ------------------------------------------------- ###
# ChIP-seq and downstream analysis
# Execute analysis on merge bam file
# Analysis executed:
# Peaks identification (SICER, MACS, ROSE)
# Motif analysis
#collate correct files for downstream analysis
File PE_sample_bam = select_first([PE_mergebam_afterbklist, uno_PE_mapping.bklist_bam, uno_PE_mapping.sorted_bam])
call macs.macs as PE_macs {
input :
bamfile=PE_sample_bam,
pvalue="1e-9",
keep_dup="auto",
egs=egs.genomesize,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS/NARROW_peaks' + '/' + basename(PE_sample_bam,'.bam') + '-p9_kd-auto',
coverage_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/COVERAGE_files/NARROW_peaks' + '/' + basename(PE_sample_bam,'.bam') + '_p9_kd-auto'
}
call util.addreadme as PE_addreadme {
input :
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS'
}
call macs.macs as PE_all {
input :
bamfile=PE_sample_bam,
pvalue="1e-9",
keep_dup="all",
egs=egs.genomesize,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS/NARROW_peaks' + '/' + basename(PE_sample_bam,'.bam') + '-p9_kd-all',
coverage_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/COVERAGE_files/NARROW_peaks' + '/' + basename(PE_sample_bam,'.bam') + '_p9_kd-all'
}
call macs.macs as PE_nomodel {
input :
bamfile=PE_sample_bam,
nomodel=true,
egs=egs.genomesize,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS/NARROW_peaks' + '/' + basename(PE_sample_bam,'.bam') + '-nm',
coverage_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/COVERAGE_files/NARROW_peaks' + '/' + basename(PE_sample_bam,'.bam') + '_nm'
}
call peaseq_util.fraggraph {
input :
bamfile=select_first([PE_merge_markdup.mkdupbam, uno_PE_mapping.mkdup_bam]),
chromsizes=samtools_faidx.chromsizes,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/COVERAGE_files/BAM_Fragments',
bam_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/BAM_files',
annotation_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/QC/Fragments'
}
call samtools.indexstats as frag_index {
input :
bamfile=fraggraph.fragbamfile,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/BAM_files'
}
call bamtogff.bamtogff as PE_bamtogff {
input :
gtffile=gtf,
chromsizes=samtools_faidx.chromsizes,
bamfile=fraggraph.fragbamfile,
bamindex=frag_index.indexbam,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/BAM_Density'
}
call sicer.sicer as PE_sicer {
input :
bedfile=fraggraph.bedpefile,
paired_end=true,
gap_size=600,
chromsizes=samtools_faidx.chromsizes,
genome_fraction=egs.genomefraction,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS/BROAD_peaks',
coverage_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/COVERAGE_files/BROAD_peaks'
}
call rose.rose as PE_rose {
input :
gtffile=gtf,
bamfile=fraggraph.fragbamfile,
bamindex=frag_index.indexbam,
bedfile_auto=PE_macs.peakbedfile,
bedfile_all=PE_all.peakbedfile,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS/STITCHED_peaks'
}
call runspp.runspp as PE_runspp {
input:
bamfile=PE_sample_bam
}
call util.peaksanno as PE_peaksanno {
input :
gtffile=gtf,
bedfile=PE_macs.peakbedfile,
chromsizes=samtools_faidx.chromsizes,
summitfile=PE_macs.summitsfile,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(PE_macs.peakbedfile),'_peaks.bed','')
}
call util.peaksanno as PE_all_peaksanno {
input :
gtffile=gtf,
bedfile=PE_all.peakbedfile,
chromsizes=samtools_faidx.chromsizes,
summitfile=PE_all.summitsfile,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(PE_all.peakbedfile),'_peaks.bed','')
}
call util.peaksanno as PE_nomodel_peaksanno {
input :
gtffile=gtf,
bedfile=PE_nomodel.peakbedfile,
chromsizes=samtools_faidx.chromsizes,
summitfile=PE_nomodel.summitsfile,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS_Annotation/NARROW_peaks' + '/' + sub(basename(PE_nomodel.peakbedfile),'_peaks.bed','')
}
call util.peaksanno as PE_sicer_peaksanno {
input :
gtffile=gtf,
bedfile=PE_sicer.scoreisland,
chromsizes=samtools_faidx.chromsizes,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/PEAKS_Annotation/BROAD_peaks'
}
# Motif Analysis
if (run_motifs) {
call motifs.motifs as PE_motifs {
input:
reference=reference,
reference_index=samtools_faidx.faidx_file,
bedfile=PE_macs.peakbedfile,
motif_databases=motif_databases,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/MOTIFS'
}
call util.flankbed as PE_flankbed {
input :
bedfile=PE_macs.summitsfile,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/MOTIFS'
}
call motifs.motifs as PE_flank {
input:
reference=reference,
reference_index=samtools_faidx.faidx_file,
bedfile=PE_flankbed.flankbedfile,
motif_databases=motif_databases,
default_location=sub(basename(PE_sample_bam),'.sorted.b.*$','') + '/MOTIFS'