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quartet_dna_quality_control_wgs_big_pipeline
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discard rename

tags/v0.2.1
LUYAO REN 2 anni fa
parent
734a3e1927
commit
b164142784
4 ha cambiato i file con 72 aggiunte e 55 eliminazioni
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  1. +10
    -6
      tasks/fastqc.wdl
  2. +12
    -8
      tasks/fastqscreen.wdl
  3. +2
    -2
      tasks/mapping.wdl
  4. +48
    -39
      workflow.wdl

+ 10
- 6
tasks/fastqc.wdl Vedi File

@@ -2,6 +2,8 @@ task fastqc {
File read1
File read2
String docker
String project
String sample
String cluster_config
String disk_size

@@ -9,8 +11,10 @@ task fastqc {
set -o pipefail
set -e
nt=$(nproc)
fastqc -t $nt -o ./ ${read1}
fastqc -t $nt -o ./ ${read2}
cp ${read1} ${project}_${sample}_R1.fastq.gz
cp ${read2} ${project}_${sample}_R2.fastq.gz
fastqc -t $nt -o ./ ${project}_${sample}_R1.fastq.gz
fastqc -t $nt -o ./ ${project}_${sample}_R2.fastq.gz
>>>

runtime {
@@ -20,9 +24,9 @@ task fastqc {
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File read1_html = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
File read1_zip = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
File read2_html = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
File read2_zip = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
File read1_html = "${project}_${sample}_R1_fastqc.html"
File read1_zip = "${project}_${sample}_R1_fastqc.zip"
File read2_html = "${project}_${sample}_R2_fastqc.html"
File read2_zip = "${project}_${sample}_R2_fastqc.html"
}
}

+ 12
- 8
tasks/fastqscreen.wdl Vedi File

@@ -4,6 +4,8 @@ task fastq_screen {
File screen_ref_dir
File fastq_screen_conf
String docker
String project
String sample
String cluster_config
String disk_size

@@ -13,8 +15,10 @@ task fastq_screen {
nt=$(nproc)
mkdir -p /cromwell_root/tmp
cp -r ${screen_ref_dir} /cromwell_root/tmp/
fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${read1}
fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${read2}
cp ${read1} ${project}_${sample}_R1.fastq.gz
cp ${read2} ${project}_${sample}_R2.fastq.gz
fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${project}_${sample}_R1.fastq.gz
fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${project}_${sample}_R2.fastq.gz
>>>

runtime {
@@ -25,11 +29,11 @@ task fastq_screen {
}
output {
File png1 = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_screen.png")
File txt1 = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_screen.txt")
File html1 = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_screen.html")
File png2 = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_screen.png")
File txt2 = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_screen.txt")
File html2 = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_screen.html")
File png1 = "${project}_${sample}_R1_screen.png"
File txt1 = "${project}_${sample}_R1_screen.txt"
File html1 = "${project}_${sample}_R1_screen.html"
File png2 = "${project}_${sample}_R2_screen.png"
File txt2 = "${project}_${sample}_R2_screen.txt"
File html2 = "${project}_${sample}_R2_screen.html"
}
}

+ 2
- 2
tasks/mapping.wdl Vedi File

@@ -7,8 +7,8 @@ task mapping {

String SENTIEON_INSTALL_DIR
String SENTIEON_LICENSE
String group = basename(fastq_1,"_R1.fastq.gz")
String sample = basename(fastq_1,"_R1.fastq.gz")
String group
String sample
String pl
String docker
String cluster_config

+ 48
- 39
workflow.wdl Vedi File

@@ -71,21 +71,6 @@ workflow {{ project_name }} {

if (fastq_1_D5!= "") {
call rename_fastq.rename_fastq as rename_fastq {
input:
fastq_1_D5=fastq_1_D5,
fastq_1_D6=fastq_1_D6,
fastq_1_F7=fastq_1_F7,
fastq_1_M8=fastq_1_M8,
fastq_2_D5=fastq_2_D5,
fastq_2_D6=fastq_2_D6,
fastq_2_F7=fastq_2_F7,
fastq_2_M8=fastq_2_M8,
project=project,
docker=DIYdocker,
cluster_config=SMALLcluster_config,
disk_size=disk_size
}

call mapping.mapping as mapping_D5 {
input:
@@ -94,8 +79,10 @@ workflow {{ project_name }} {
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
fastq_1=rename_fastq.fastq_1_D5_renamed,
fastq_2=rename_fastq.fastq_2_D5_renamed,
fastq_1=fastq_1_D5,
fastq_2=fastq_2_D5,
group=project,
sample='LCL5',
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -103,8 +90,10 @@ workflow {{ project_name }} {

call fastqc.fastqc as fastqc_D5 {
input:
read1=rename_fastq.fastq_1_D5_renamed,
read2=rename_fastq.fastq_2_D5_renamed,
read1=fastq_1_D5,
read2=fastq_2_D5,
project=project,
sample="LCL5",
docker=FASTQCdocker,
cluster_config=BIGcluster_config,
disk_size=disk_size
@@ -112,8 +101,10 @@ workflow {{ project_name }} {

call fastqscreen.fastq_screen as fastqscreen_D5 {
input:
read1=rename_fastq.fastq_1_D5_renamed,
read2=rename_fastq.fastq_2_D5_renamed,
read1=fastq_1_D5,
read2=fastq_2_D5,
project=project,
sample="LCL5",
screen_ref_dir=screen_ref_dir,
fastq_screen_conf=fastq_screen_conf,
docker=FASTQSCREENdocker,
@@ -231,8 +222,10 @@ workflow {{ project_name }} {
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
fastq_1=rename_fastq.fastq_1_D6_renamed,
fastq_2=rename_fastq.fastq_2_D6_renamed,
fastq_1=fastq_1_D6,
fastq_2=fastq_2_D6,
group=project,
sample='LCL6',
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -240,8 +233,10 @@ workflow {{ project_name }} {

call fastqc.fastqc as fastqc_D6 {
input:
read1=rename_fastq.fastq_1_D6_renamed,
read2=rename_fastq.fastq_2_D6_renamed,
read1=fastq_1_D6,
read2=fastq_2_D6,
project=project,
sample="LCL6",
docker=FASTQCdocker,
cluster_config=BIGcluster_config,
disk_size=disk_size
@@ -249,8 +244,10 @@ workflow {{ project_name }} {

call fastqscreen.fastq_screen as fastqscreen_D6 {
input:
read1=rename_fastq.fastq_1_D6_renamed,
read2=rename_fastq.fastq_2_D6_renamed,
read1=fastq_1_D6,
read2=fastq_2_D6,
project=project,
sample="LCL6",
screen_ref_dir=screen_ref_dir,
fastq_screen_conf=fastq_screen_conf,
docker=FASTQSCREENdocker,
@@ -368,8 +365,10 @@ workflow {{ project_name }} {
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
fastq_1=rename_fastq.fastq_1_F7_renamed,
fastq_2=rename_fastq.fastq_2_F7_renamed,
fastq_1=fastq_1_F7,
fastq_2=fastq_2_F7,
group=project,
sample='LCL7',
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -377,8 +376,10 @@ workflow {{ project_name }} {

call fastqc.fastqc as fastqc_F7 {
input:
read1=rename_fastq.fastq_1_F7_renamed,
read2=rename_fastq.fastq_2_F7_renamed,
read1=fastq_1_F7,
read2=fastq_2_F7,
project=project,
sample="LCL7",
docker=FASTQCdocker,
cluster_config=BIGcluster_config,
disk_size=disk_size
@@ -386,8 +387,10 @@ workflow {{ project_name }} {

call fastqscreen.fastq_screen as fastqscreen_F7 {
input:
read1=rename_fastq.fastq_1_F7_renamed,
read2=rename_fastq.fastq_2_F7_renamed,
read1=fastq_1_F7,
read2=fastq_2_F7,
project=project,
sample="LCL7",
screen_ref_dir=screen_ref_dir,
fastq_screen_conf=fastq_screen_conf,
docker=FASTQSCREENdocker,
@@ -505,8 +508,10 @@ workflow {{ project_name }} {
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
fastq_1=rename_fastq.fastq_1_M8_renamed,
fastq_2=rename_fastq.fastq_2_M8_renamed,
fastq_1=fastq_1_M8,
fastq_2=fastq_2_M8,
group=project,
sample='LCL8',
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -514,8 +519,10 @@ workflow {{ project_name }} {

call fastqc.fastqc as fastqc_M8 {
input:
read1=rename_fastq.fastq_1_M8_renamed,
read2=rename_fastq.fastq_2_M8_renamed,
read1=fastq_1_M8,
read2=fastq_2_M8,
project=project,
sample="LCL8",
docker=FASTQCdocker,
cluster_config=BIGcluster_config,
disk_size=disk_size
@@ -523,8 +530,10 @@ workflow {{ project_name }} {

call fastqscreen.fastq_screen as fastqscreen_M8 {
input:
read1=rename_fastq.fastq_1_M8_renamed,
read2=rename_fastq.fastq_2_M8_renamed,
read1=fastq_1_M8,
read2=fastq_2_M8,
project=project,
sample="LCL8",
screen_ref_dir=screen_ref_dir,
fastq_screen_conf=fastq_screen_conf,
docker=FASTQSCREENdocker,

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