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peaseq-control.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: 'modupeore.adetunji@stjude.org',
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
Array[String]? control_sraid
Array[File]? control_R1_fastq
Array[File]? control_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"]
}
control_sraid: {
description: 'One or more input/control SRA (Sequence Read Archive) run identifiers',
group: 'input_genomic_data',
help: 'Input publicly available FASTQs (SRRs). Multiple SRRs are separated by commas (,).',
example: 'SRR12345678'
}
control_R1_fastq: {
description: 'One or more input/control R1 FASTQs',
group: 'input_genomic_data',
help: 'Upload zipped FASTQ files.',
patterns: ["*.fq.gz", "*.fastq.gz"]
}
control_R2_fastq: {
description: 'One or more input/control 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
if ( defined(control_sraid) ) {
# Download control file(s) from SRA database
# outputs:
# fastqdump.fastqfile : downloaded sample files in fastq.gz format
Array[String] c_sra = [1] #buffer to allow for sra_id optionality
Array[String] c_sraid = select_first([control_sraid, c_sra])
scatter (eachsra in c_sraid) {
call sra.fastqdump as c_fastqdump {
input :
sra_id=eachsra,
cloud=false
}
File c_R1end = select_first([c_fastqdump.R1end, c_sra[0]])
File c_R2end = select_first([c_fastqdump.R2end, c_sra[0]])
} # end scatter each sra
Array[File] control_R1_srafile = c_R1end
Array[File] control_R2_srafile = c_R2end
} # end if control_sra_id
# 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])
}
if ( defined(control_R1_fastq) ) {
Array[String] c_string_fastq = [1] #buffer to allow for fastq optionality
Array[File] c_R1_fastq = select_first([control_R1_fastq, c_string_fastq])
Array[File] control_R1_fastqfile = c_R1_fastq
Array[File] c_R2_fastq = select_first([control_R2_fastq, c_string_fastq])
Array[File] control_R2_fastqfile = c_R2_fastq
# Order FASTQs
if (length(control_R1_fastqfile) > 1) {
call peaseq_util.sortfiles as c_R1_sorted { input: fastqfiles=control_R1_fastqfile }
call peaseq_util.sortfiles as c_R2_sorted { input: fastqfiles=control_R2_fastqfile }
}
Array[File] control_R1_fastqfiles = select_first([c_R1_sorted.allfiles, control_R1_fastqfile])
Array[File] control_R2_fastqfiles = select_first([c_R2_sorted.allfiles, control_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]))
Array[File] original_control_R1 = flatten(select_all([control_R1_srafile, control_R1_fastqfiles]))
Array[File] original_control_R2 = flatten(select_all([control_R2_srafile, control_R2_fastqfiles]))
Array[File] original_all_control_fastqfiles = flatten(select_all([control_R1_srafile, control_R1_fastqfiles,control_R2_srafile, control_R2_fastqfiles]))
# transpose to paired-end tuples
Array[Pair[File, File]] original_sample_fastqfiles = zip(original_sample_R1, original_sample_R2)
Array[Pair[File, File]] original_control_fastqfiles = zip(original_control_R1, original_control_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
Boolean multi_control_fastqpair = if length(original_control_fastqfiles) > 1 then true else false
Boolean one_control_fastqpair = if length(original_control_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_s_indv_fastqc {
input :
inputfile=eachfastq,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/FastQC' else 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/FastQC'
}
}
scatter (eachfastq in original_all_control_fastqfiles) {
call fastqc.fastqc as spikein_c_indv_fastqc {
input :
inputfile=eachfastq,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/FastQC' else 'CONTROL/' + 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_s_indv_R1_bfs {
input :
fastqfile=fastqpair.left,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats' else 'SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats'
}
call bowtie.spikein_PE as spikein_s_indv_map {
input :
fastqfile=fastqpair.left,
fastqfile_R2=fastqpair.right,
metricsfile=spikein_s_indv_R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_spikein_bowtie_index,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats' else 'SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats'
}
}
scatter (fastqpair in original_control_fastqfiles) {
call util.basicfastqstats as spikein_c_indv_R1_bfs {
input :
fastqfile=fastqpair.left,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats' else 'CONTROL/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats'
}
call bowtie.spikein_PE as spikein_c_indv_map {
input :
fastqfile=fastqpair.left,
fastqfile_R2=fastqpair.right,
metricsfile=spikein_c_indv_R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_spikein_bowtie_index,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/SpikeIn/SummaryStats' else 'CONTROL/' + 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_s_R1_sorted { input: fastqfiles=spikein_s_indv_map.unaligned_1 }
call peaseq_util.sortfiles as spikein_s_R2_sorted { input: fastqfiles=spikein_s_indv_map.unaligned_2 }
}
if (length(original_control_R1) > 1) {
call peaseq_util.sortfiles as spikein_c_R1_sorted { input: fastqfiles=spikein_c_indv_map.unaligned_1 }
call peaseq_util.sortfiles as spikein_c_R2_sorted { input: fastqfiles=spikein_c_indv_map.unaligned_2 }
}
Array[File] spikein_sample_R1 = select_first([spikein_s_R1_sorted.allfiles, spikein_s_indv_map.unaligned_1])
Array[File] spikein_sample_R2 = select_first([spikein_s_R2_sorted.allfiles, spikein_s_indv_map.unaligned_2])
Array[File] spikein_control_R1 = select_first([spikein_c_R1_sorted.allfiles, spikein_c_indv_map.unaligned_1])
Array[File] spikein_control_R2 = select_first([spikein_c_R2_sorted.allfiles, spikein_c_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] spikein_all_control_fastqfiles = flatten(select_all([spikein_control_R1, spikein_control_R2]))
Array[Pair[File, File]] spikein_control_fastqfiles = zip(spikein_control_R1, spikein_control_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])
Array[File] all_control_fastqfiles = select_first([spikein_all_control_fastqfiles, original_all_control_fastqfiles])
Array[Pair[File, File]] control_fastqfiles = select_first([spikein_control_fastqfiles, original_control_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 s_indv_fastqc {
input :
inputfile=eachfastq,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call util.basicfastqstats as indv_s_bfs {
input :
fastqfile=eachfastq,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
call mapping.mapping as indv_s_mapping {
input :
fastqfile=eachfastq,
index_files=actual_bowtie_index,
metricsfile=indv_s_bfs.metrics_out,
blacklist=blacklist,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files' else 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files'
}
call fastqc.fastqc as indv_s_bamfqc {
input :
inputfile=indv_s_mapping.sorted_bam,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call runspp.runspp as indv_s_runspp {
input:
bamfile=select_first([indv_s_mapping.bklist_bam, indv_s_mapping.sorted_bam])
}
call bedtools.bamtobed as indv_s_bamtobed {
input:
bamfile=select_first([indv_s_mapping.bklist_bam, indv_s_mapping.sorted_bam])
}
call util.evalstats as indv_s_summarystats {
input:
fastq_type="PEAseq Sample FASTQ",
bambed=indv_s_bamtobed.bedfile,
sppfile=indv_s_runspp.spp_out,
fastqczip=s_indv_fastqc.zipfile,
bamflag=indv_s_mapping.bam_stats,
rmdupflag=indv_s_mapping.mkdup_stats,
bkflag=indv_s_mapping.bklist_stats,
fastqmetrics=indv_s_bfs.metrics_out,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/SummaryStats' else 'SAMPLE/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/SummaryStats'
}
} # end scatter (for eachfastq : samples)
# MERGE BAM files
# Execute analysis on merge bam file
# Analysis executed:
# Merge BAM (SE mode : for each fastq paired-end)
call util.mergehtml as SE_s_mergehtml {
input:
htmlfiles=indv_s_summarystats.xhtml,
txtfiles=indv_s_summarystats.textfile,
default_location='SAMPLE',
outputfile = 'AllCases-summary-stats.html'
}
call samtools.mergebam as SE_s_mergebam {
input:
bamfiles=indv_s_mapping.sorted_bam,
metricsfiles=indv_s_bfs.metrics_out,
default_location=if multi_fastqpair then 'SAMPLE/' + 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'SAMPLE/' + sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files',
outputfile='AllCases_' + length(all_sample_fastqfiles) + 'fastqs_SE.sorted.bam'
}
call fastqc.fastqc as SE_s_mergebamfqc {
input:
inputfile=SE_s_mergebam.mergebam,
default_location= if multi_fastqpair then 'SAMPLE/' + 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs/single-end_mode/QC/FastQC' else 'SAMPLE/' + 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_s_mergeindexstats {
input:
bamfile=SE_s_mergebam.mergebam,
default_location=if multi_fastqpair then 'SAMPLE/' + 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'SAMPLE/' + 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_s_merge_rmblklist {
input :
fileA=SE_s_mergebam.mergebam,
fileB=blacklist_file,
default_location=if multi_fastqpair then 'SAMPLE/' + 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'SAMPLE/' + 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_s_merge_bklist {
input :
bamfile=SE_s_merge_rmblklist.intersect_out,
default_location=if multi_fastqpair then 'SAMPLE/' + 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'SAMPLE/' + 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_s_mergebam_afterbklist = select_first([SE_s_merge_rmblklist.intersect_out, SE_s_mergebam.mergebam])
call samtools.markdup as SE_s_merge_markdup {
input :
bamfile=SE_s_mergebam_afterbklist,
default_location=if multi_fastqpair then 'SAMPLE/' + 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'SAMPLE/' + 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_s_merge_mkdup {
input :
bamfile=SE_s_merge_markdup.mkdupbam,
default_location=if multi_fastqpair then 'SAMPLE/' + 'AllCases_' + length(sample_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'SAMPLE/' + sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
# CONTROL FASTQ FILES
scatter (eachfastq in all_control_fastqfiles) {
call fastqc.fastqc as c_indv_fastqc {
input :
inputfile=eachfastq,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else 'CONTROL/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call util.basicfastqstats as indv_c_bfs {
input :
fastqfile=eachfastq,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else 'CONTROL/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
call mapping.mapping as indv_c_mapping {
input :
fastqfile=eachfastq,
index_files=actual_bowtie_index,
metricsfile=indv_c_bfs.metrics_out,
blacklist=blacklist,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files' else 'CONTROL/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files'
}
call fastqc.fastqc as indv_c_bamfqc {
input :
inputfile=indv_c_mapping.sorted_bam,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else 'CONTROL/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call runspp.runspp as indv_c_runspp {
input:
bamfile=select_first([indv_c_mapping.bklist_bam, indv_c_mapping.sorted_bam])
}
call bedtools.bamtobed as indv_c_bamtobed {
input:
bamfile=select_first([indv_c_mapping.bklist_bam, indv_c_mapping.sorted_bam])
}
call util.evalstats as indv_c_summarystats {
input:
fastq_type="PEAseq Control FASTQ",
bambed=indv_c_bamtobed.bedfile,
sppfile=indv_c_runspp.spp_out,
fastqczip=c_indv_fastqc.zipfile,
bamflag=indv_c_mapping.bam_stats,
rmdupflag=indv_c_mapping.mkdup_stats,
bkflag=indv_c_mapping.bklist_stats,
fastqmetrics=indv_c_bfs.metrics_out,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/SummaryStats' else 'CONTROL/' + sub(basename(eachfastq),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/SummaryStats'
}
} # end scatter (for eachfastq : control)
# MERGE BAM files
# Execute analysis on merge bam file
# Analysis executed:
# Merge BAM (SE mode : for each fastq paired-end)
call util.mergehtml as SE_c_mergehtml {
input:
fastq_type="PEAseq Control FASTQs",
htmlfiles=indv_c_summarystats.xhtml,
txtfiles=indv_c_summarystats.textfile,
default_location='CONTROL',
outputfile = 'AllControls-summary-stats.html'
}
call samtools.mergebam as SE_c_mergebam {
input:
bamfiles=indv_c_mapping.sorted_bam,
metricsfiles=indv_c_bfs.metrics_out,
default_location=if multi_control_fastqpair then 'CONTROL/' + 'AllControls_' + length(control_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'CONTROL/' + sub(basename(control_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files',
outputfile='AllControls_' + length(all_control_fastqfiles) + 'fastqs_SE.sorted.bam'
}
call fastqc.fastqc as SE_c_mergebamfqc {
input:
inputfile=SE_c_mergebam.mergebam,
default_location=if multi_control_fastqpair then 'CONTROL/' + 'AllControls_' + length(control_fastqfiles) + 'fastqpairs/single-end_mode/QC/FastQC' else 'CONTROL/' + sub(basename(control_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/QC/FastQC'
}
call samtools.indexstats as SE_c_mergeindexstats {
input:
bamfile=SE_c_mergebam.mergebam,
default_location=if multi_control_fastqpair then 'CONTROL/' + 'AllControls_' + length(control_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'CONTROL/' + sub(basename(control_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 c_string_blacklist = "" #buffer to allow for blacklist optionality
File c_blacklist_file = select_first([blacklist, c_string_blacklist])
call bedtools.intersect as SE_c_merge_rmblklist {
input :
fileA=SE_c_mergebam.mergebam,
fileB=c_blacklist_file,
default_location=if multi_control_fastqpair then 'CONTROL/' + 'AllControls_' + length(control_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'CONTROL/' + sub(basename(control_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_c_merge_bklist {
input :
bamfile=SE_c_merge_rmblklist.intersect_out,
default_location=if multi_control_fastqpair then 'CONTROL/' + 'AllControls_' + length(control_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'CONTROL/' + sub(basename(control_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
} # end if blacklist provided
File SE_c_mergebam_afterbklist = select_first([SE_c_merge_rmblklist.intersect_out, SE_c_mergebam.mergebam])
call samtools.markdup as SE_c_merge_markdup {
input :
bamfile=SE_c_mergebam_afterbklist,
default_location=if multi_control_fastqpair then 'CONTROL/' + 'AllControls_' + length(control_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'CONTROL/' + sub(basename(control_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/single-end_mode/BAM_files'
}
call samtools.indexstats as SE_c_merge_mkdup {
input :
bamfile=SE_c_merge_markdup.mkdupbam,
default_location=if multi_control_fastqpair then 'CONTROL/' + 'AllControls_' + length(control_fastqfiles) + 'fastqpairs/single-end_mode/BAM_files' else 'CONTROL/' + sub(basename(control_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 s_indv_R1_bfs {
input :
fastqfile=fastqpair.left,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else 'SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
call mapping.mapping as s_indv_PE_mapping {
input :
fastqfile=fastqpair.left,
fastqfile_R2=fastqpair.right,
metricsfile=s_indv_R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_bowtie_index,
blacklist=blacklist,
paired_end=true,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files' else 'SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files'
}
call fastqc.fastqc as s_indv_PE_bamfqc {
input :
inputfile=s_indv_PE_mapping.sorted_bam,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else 'SAMPLE/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call runspp.runspp as s_indv_PE_runspp {
input:
bamfile=select_first([s_indv_PE_mapping.bklist_bam, s_indv_PE_mapping.sorted_bam])
}
call peaseq_util.pe_bamtobed as s_indv_PE_bamtobed {
input:
bamfile=select_first([s_indv_PE_mapping.bklist_bam, s_indv_PE_mapping.sorted_bam])
}
call util.evalstats as s_indv_PE_summarystats {
input:
fastq_type="PEAseq Sample FASTQ",
bambed=s_indv_PE_bamtobed.bedfile,
sppfile=s_indv_PE_runspp.spp_out,
fastqczip=s_indv_PE_bamfqc.zipfile,
bamflag=s_indv_PE_mapping.bam_stats,
rmdupflag=s_indv_PE_mapping.mkdup_stats,
bkflag=s_indv_PE_mapping.bklist_stats,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else '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 (AllCases_<number>_mapped)
# merge bam files and perform fasTQC if more than one is provided
call util.mergehtml as s_PE_mergehtml {
input:
htmlfiles=s_indv_PE_summarystats.xhtml,
txtfiles=s_indv_PE_summarystats.textfile,
default_location='SAMPLE',
outputfile = 'AllCases_PEmode_peaseq-summary-stats.html'
}
call peaseq_util.pe_mergehtml as s_final_mergehtml {
input:
pe_htmlfiles=s_indv_PE_summarystats.xhtml,
pe_txtfiles=s_indv_PE_summarystats.textfile,
se_htmlfiles=indv_s_summarystats.xhtml,
se_txtfiles=indv_s_summarystats.textfile,
default_location='SAMPLE',
outputfile = 'AllCases-summary-stats.html'
}
call samtools.mergebam as s_PE_mergebam {
input:
bamfiles=s_indv_PE_mapping.as_sortedbam,
metricsfiles=indv_s_bfs.metrics_out,
paired_end=true,
default_location='SAMPLE/' + 'AllCases_' + length(s_indv_PE_mapping.sorted_bam) + 'fastqpairs/BAM_files',
outputfile='AllCases_' + length(sample_fastqfiles) + 'fastqpairs.sorted.bam',
fixmatefile='AllCases_' + length(sample_fastqfiles) + 'fastqpairs.fixmate.bam'
}
call fastqc.fastqc as s_PE_mergebamfqc {
input:
inputfile=s_PE_mergebam.mergebam,
default_location='SAMPLE/' + sub(basename(s_PE_mergebam.mergebam),'.sorted.b.*$','') + '/QC/FastQC'
}
call samtools.indexstats as s_PE_mergeindexstats {
input:
bamfile=s_PE_mergebam.mergebam,
default_location='SAMPLE/' + sub(basename(s_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
if ( defined(blacklist) ) {
# remove blacklist regions
String s_string_pe_blacklist = "" #buffer to allow for blacklist optionality
File s_blacklist_pe = select_first([blacklist, s_string_pe_blacklist])
String s_string_pe_fixmate = "" #buffer to allow for blacklist optionality
File s_fixmate_pe = select_first([s_PE_mergebam.fixmatemergebam, s_string_pe_fixmate])
call bedtools.pairtobed as s_PE_merge_rmblklist {
input :
fileA=s_fixmate_pe,
fileB=s_blacklist_pe,
default_location='SAMPLE/' + sub(basename(s_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
call samtools.indexstats as s_PE_merge_bklist {
input :
bamfile=s_PE_merge_rmblklist.pairtobed_out,
default_location='SAMPLE/' + sub(basename(s_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
} # end if blacklist provided
File s_PE_mergebam_afterbklist = select_first([s_PE_merge_rmblklist.pairtobed_out, s_PE_mergebam.mergebam])
call samtools.markdup as s_PE_merge_markdup {
input :
bamfile=s_PE_mergebam_afterbklist,
default_location='SAMPLE/' + sub(basename(s_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
call samtools.indexstats as s_PE_merge_mkdup {
input :
bamfile=s_PE_merge_markdup.mkdupbam,
default_location='SAMPLE/' + sub(basename(s_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
} # end if length(fastqfiles) > 1: multi_fastqpair
# CONTROL FASTQ FILES
if ( multi_control_fastqpair ) {
scatter (fastqpair in control_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 c_indv_R1_bfs {
input :
fastqfile=fastqpair.left,
default_location=if multi_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else 'CONTROL/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
call mapping.mapping as c_indv_PE_mapping {
input :
fastqfile=fastqpair.left,
fastqfile_R2=fastqpair.right,
metricsfile=c_indv_R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_bowtie_index,
blacklist=blacklist,
paired_end=true,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files' else 'CONTROL/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files'
}
call fastqc.fastqc as c_indv_PE_bamfqc {
input :
inputfile=c_indv_PE_mapping.sorted_bam,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC' else 'CONTROL/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call runspp.runspp as c_indv_PE_runspp {
input:
bamfile=select_first([c_indv_PE_mapping.bklist_bam, c_indv_PE_mapping.sorted_bam])
}
call peaseq_util.pe_bamtobed as c_indv_PE_bamtobed {
input:
bamfile=select_first([c_indv_PE_mapping.bklist_bam, c_indv_PE_mapping.sorted_bam])
}
call util.evalstats as c_indv_PE_summarystats {
input:
fastq_type="PEAseq Control FASTQ",
bambed=c_indv_PE_bamtobed.bedfile,
sppfile=c_indv_PE_runspp.spp_out,
fastqczip=c_indv_PE_bamfqc.zipfile,
bamflag=c_indv_PE_mapping.bam_stats,
rmdupflag=c_indv_PE_mapping.mkdup_stats,
bkflag=c_indv_PE_mapping.bklist_stats,
default_location=if multi_control_fastqpair then 'CONTROL/individual_fastqs/' + sub(basename(fastqpair.left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else 'CONTROL/' + 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 (AllControl_<number>_mapped)
# merge bam files and perform fasTQC if more than one is provided
call util.mergehtml as c_PE_mergehtml {
input:
htmlfiles=c_indv_PE_summarystats.xhtml,
txtfiles=c_indv_PE_summarystats.textfile,
default_location='CONTROL',
outputfile = 'AllControl_PEmode_peaseq-summary-stats.html'
}
call peaseq_util.pe_mergehtml as c_final_mergehtml {
input:
fastq_type = "PEAseq Control FASTQs",
pe_htmlfiles=c_indv_PE_summarystats.xhtml,
pe_txtfiles=c_indv_PE_summarystats.textfile,
se_htmlfiles=indv_c_summarystats.xhtml,
se_txtfiles=indv_c_summarystats.textfile,
default_location='CONTROL',
outputfile = 'AllControls-summary-stats.html'
}
call samtools.mergebam as c_PE_mergebam {
input:
bamfiles=c_indv_PE_mapping.as_sortedbam,
metricsfiles=indv_c_bfs.metrics_out,
paired_end=true,
default_location = 'CONTROL/' + 'AllControls_' + length(c_indv_PE_mapping.sorted_bam) + 'fastqpairs/BAM_files',
outputfile = 'AllControls_' + length(control_fastqfiles) + 'fastqpairs.sorted.bam',
fixmatefile = 'AllControls_' + length(control_fastqfiles) + 'fastqpairs.fixmate.bam'
}
call fastqc.fastqc as c_PE_mergebamfqc {
input:
inputfile=c_PE_mergebam.mergebam,
default_location='CONTROL/' + sub(basename(c_PE_mergebam.mergebam),'.sorted.b.*$','') + '/QC/FastQC'
}
call samtools.indexstats as c_PE_mergeindexstats {
input:
bamfile=c_PE_mergebam.mergebam,
default_location='CONTROL/' + sub(basename(c_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
if ( defined(blacklist) ) {
# remove blacklist regions
String c_string_pe_blacklist = "" #buffer to allow for blacklist optionality
File c_blacklist_pe = select_first([blacklist, c_string_pe_blacklist])
String c_string_pe_fixmate = "" #buffer to allow for blacklist optionality
File c_fixmate_pe = select_first([c_PE_mergebam.fixmatemergebam, c_string_pe_fixmate])
call bedtools.pairtobed as c_PE_merge_rmblklist {
input :
fileA=c_fixmate_pe,
fileB=c_blacklist_pe,
default_location='CONTROL/' + sub(basename(c_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
call samtools.indexstats as c_PE_merge_bklist {
input :
bamfile=c_PE_merge_rmblklist.pairtobed_out,
default_location='CONTROL/' + sub(basename(c_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
} # end if blacklist provided
File c_PE_mergebam_afterbklist = select_first([c_PE_merge_rmblklist.pairtobed_out, c_PE_mergebam.mergebam])
call samtools.markdup as c_PE_merge_markdup {
input :
bamfile=c_PE_mergebam_afterbklist,
default_location='CONTROL/' + sub(basename(c_PE_mergebam.mergebam),'.sorted.b.*$','') + '/BAM_files'
}
call samtools.indexstats as c_PE_merge_mkdup {
input :
bamfile=c_PE_merge_markdup.mkdupbam,
default_location='CONTROL/' + sub(basename(c_PE_mergebam.mergebam),'.sorted.b.*$','') + '/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 s_R1_bfs {
input :
fastqfile=sample_fastqfiles[0].left,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats' else 'SAMPLE/' + sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/SummaryStats'
}
call mapping.mapping as s_uno_PE_mapping {
input :
fastqfile=sample_fastqfiles[0].left,
fastqfile_R2=sample_fastqfiles[0].right,
metricsfile=s_R1_bfs.metrics_out,
insert_size=insertsize,
strandedness=strandedness,
index_files=actual_bowtie_index,
blacklist=blacklist,
paired_end=true,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files' else 'SAMPLE/' + sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/BAM_files'
}
call fastqc.fastqc as s_uno_PE_bamfqc {
input :
inputfile=s_uno_PE_mapping.sorted_bam,
default_location=if multi_fastqpair then 'SAMPLE/individual_fastqs/' + sub(basename(s_uno_PE_mapping.sorted_bam),'.sorted.bam','') + '/QC/FastQC' else 'SAMPLE/' + sub(basename(sample_fastqfiles[0].left),'_R?[12]_....f.*q.gz|_R?[12].f.*q.gz','') + '/QC/FastQC'
}
call peaseq_util.pe_bamtobed as s_uno_PE_bamtobed {
input:
bamfile=select_first([s_uno_PE_mapping.bklist_bam, s_uno_PE_mapping.sorted_bam])
}
} # end if length(fastqfiles) == 1: one_fastqpair