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quartet_dna_quality_control_wgs_big_pipeline
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change name

tags/v0.1.1
LUYAO REN vor 3 Jahren
Ursprung
48c3f31d75
Commit
40b152efeb
2 geänderte Dateien mit 49 neuen und 62 gelöschten Zeilen
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  1. +17
    -26
      tasks/multiqc.wdl
  2. +32
    -36
      workflow.wdl

+ 17
- 26
tasks/multiqc.wdl Datei anzeigen

@@ -1,15 +1,13 @@
task multiqc {

Array[File]? read1_zip
Array[File]? read2_zip
Array[File] read1_zip
Array[File] read2_zip

Array[File]? txt1
Array[File]? txt2
Array[File] txt1
Array[File] txt2

Array[File] summary

Array[File]? zip

String docker
String cluster_config
String disk_size
@@ -17,26 +15,19 @@ task multiqc {
command <<<
set -o pipefail
set -e
if [ ${zip} ];then
mkdir -p /cromwell_root/tmp/fastqc
mkdir -p /cromwell_root/tmp/fastqscreen
mkdir -p /cromwell_root/tmp/benchmark

cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
cp ${sep=" " summary} /cromwell_root/tmp/benchmark

multiqc /cromwell_root/tmp/

cat multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
cat multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt
cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
else
mkdir -p /cromwell_root/tmp/benchmark
cp ${sep=" " summary} /cromwell_root/tmp/benchmark
multiqc /cromwell_root/tmp/
cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
fi
mkdir -p /cromwell_root/tmp/fastqc
mkdir -p /cromwell_root/tmp/fastqscreen
mkdir -p /cromwell_root/tmp/benchmark

cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
cp ${sep=" " summary} /cromwell_root/tmp/benchmark

multiqc /cromwell_root/tmp/

cat multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
cat multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt
cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
>>>


+ 32
- 36
workflow.wdl Datei anzeigen

@@ -73,8 +73,8 @@ workflow {{ project_name }} {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
group="D5",
sample="D5",
group="LCL5",
sample="LCL5",
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
@@ -110,7 +110,7 @@ workflow {{ project_name }} {
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_D5.sorted_bam,
sorted_bam_index=mapping_D5.sorted_bam_index,
sample="D5",
sample="LCL5",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -132,7 +132,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
Dedup_bam=Dedup_D5.Dedup_bam,
Dedup_bam_index=Dedup_D5.Dedup_bam_index,
sample="D5",
sample="LCL5",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -144,7 +144,7 @@ workflow {{ project_name }} {
wgs_metrics_algo=deduped_Metrics_D5.deduped_wgsmetrics,
aln_metrics=deduped_Metrics_D5.dedeuped_aln_metrics,
is_metrics=deduped_Metrics_D5.deduped_is_metrics,
sample="D5",
sample="LCL5",
docker=SENTIEONdocker,
cluster_config=SMALLcluster_config,
disk_size=disk_size
@@ -159,7 +159,7 @@ workflow {{ project_name }} {
Dedup_bam_index=Dedup_D5.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
sample="D5",
sample="LCL5",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -176,7 +176,7 @@ workflow {{ project_name }} {
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
sample="D5",
sample="LCL5",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -189,7 +189,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
recaled_bam=BQSR_D5.recaled_bam,
recaled_bam_index=BQSR_D5.recaled_bam_index,
sample="D5",
sample="LCL5",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -218,8 +218,8 @@ workflow {{ project_name }} {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
group="D6",
sample="D6",
group="LCL6",
sample="LCL6",
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
@@ -255,7 +255,7 @@ workflow {{ project_name }} {
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_D6.sorted_bam,
sorted_bam_index=mapping_D6.sorted_bam_index,
sample="D6",
sample="LCL6",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -277,7 +277,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
Dedup_bam=Dedup_D6.Dedup_bam,
Dedup_bam_index=Dedup_D6.Dedup_bam_index,
sample="D6",
sample="LCL6",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -289,7 +289,7 @@ workflow {{ project_name }} {
wgs_metrics_algo=deduped_Metrics_D6.deduped_wgsmetrics,
aln_metrics=deduped_Metrics_D6.dedeuped_aln_metrics,
is_metrics=deduped_Metrics_D6.deduped_is_metrics,
sample="D6",
sample="LCL6",
docker=SENTIEONdocker,
cluster_config=SMALLcluster_config,
disk_size=disk_size
@@ -304,7 +304,7 @@ workflow {{ project_name }} {
Dedup_bam_index=Dedup_D6.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
sample="D6",
sample="LCL6",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -321,7 +321,7 @@ workflow {{ project_name }} {
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
sample="D6",
sample="LCL6",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -334,7 +334,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
recaled_bam=BQSR_D6.recaled_bam,
recaled_bam_index=BQSR_D6.recaled_bam_index,
sample="D6",
sample="LCL6",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -363,8 +363,8 @@ workflow {{ project_name }} {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
group="F7",
sample="F7",
group="LCL7",
sample="LCL7",
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
@@ -400,7 +400,7 @@ workflow {{ project_name }} {
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_F7.sorted_bam,
sorted_bam_index=mapping_F7.sorted_bam_index,
sample="F7",
sample="LCL7",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -422,7 +422,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
Dedup_bam=Dedup_F7.Dedup_bam,
Dedup_bam_index=Dedup_F7.Dedup_bam_index,
sample="F7",
sample="LCL7",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -434,7 +434,7 @@ workflow {{ project_name }} {
wgs_metrics_algo=deduped_Metrics_F7.deduped_wgsmetrics,
aln_metrics=deduped_Metrics_F7.dedeuped_aln_metrics,
is_metrics=deduped_Metrics_F7.deduped_is_metrics,
sample="F7",
sample="LCL7",
docker=SENTIEONdocker,
cluster_config=SMALLcluster_config,
disk_size=disk_size
@@ -449,7 +449,7 @@ workflow {{ project_name }} {
Dedup_bam_index=Dedup_F7.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
sample="F7",
sample="LCL7",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -466,7 +466,7 @@ workflow {{ project_name }} {
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
sample="F7",
sample="LCL7",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -479,7 +479,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
recaled_bam=BQSR_F7.recaled_bam,
recaled_bam_index=BQSR_F7.recaled_bam_index,
sample="F7",
sample="LCL7",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -508,8 +508,8 @@ workflow {{ project_name }} {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
group="M8",
sample="M8",
group="LCL8",
sample="LCL8",
pl="ILLUMINAL",
fasta=fasta,
ref_dir=ref_dir,
@@ -545,7 +545,7 @@ workflow {{ project_name }} {
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_M8.sorted_bam,
sorted_bam_index=mapping_M8.sorted_bam_index,
sample="M8",
sample="LCL8",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -567,7 +567,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
Dedup_bam=Dedup_M8.Dedup_bam,
Dedup_bam_index=Dedup_M8.Dedup_bam_index,
sample="M8",
sample="LCL8",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -579,7 +579,7 @@ workflow {{ project_name }} {
wgs_metrics_algo=deduped_Metrics_M8.deduped_wgsmetrics,
aln_metrics=deduped_Metrics_M8.dedeuped_aln_metrics,
is_metrics=deduped_Metrics_M8.deduped_is_metrics,
sample="M8",
sample="LCL8",
docker=SENTIEONdocker,
cluster_config=SMALLcluster_config,
disk_size=disk_size
@@ -594,7 +594,7 @@ workflow {{ project_name }} {
Dedup_bam_index=Dedup_M8.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
sample="M8",
sample="LCL8",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -611,7 +611,7 @@ workflow {{ project_name }} {
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
sample="M8",
sample="LCL8",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -624,7 +624,7 @@ workflow {{ project_name }} {
ref_dir=ref_dir,
recaled_bam=BQSR_M8.recaled_bam,
recaled_bam_index=BQSR_M8.recaled_bam_index,
sample="M8",
sample="LCL8",
docker=SENTIEONdocker,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -660,9 +660,6 @@ workflow {{ project_name }} {

Array[File] benchmark_summary = [benchmark_D5.summary, benchmark_D6.summary, benchmark_F7.summary, benchmark_M8.summary]

Array[File] qualimap_zip = [qualimap_D5.zip, qualimap_D6.zip, qualimap_F7.zip, qualimap_M8.zip]


call multiqc.multiqc as multiqc_big {
input:
read1_zip=fastqc_read1_zip,
@@ -670,7 +667,6 @@ workflow {{ project_name }} {
txt1=fastqscreen_txt1,
txt2=fastqscreen_txt2,
summary=benchmark_summary,
zip=qualimap_zip,
docker=MULTIQCdocker,
cluster_config=SMALLcluster_config,
disk_size=disk_size

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