Преглед изворни кода

revise workflow

tags/v0.1.0
stead99 пре 4 година
родитељ
комит
f2ad8a81f3
5 измењених фајлова са 62 додато и 33 уклоњено
  1. +1
    -1
      defaults
  2. +1
    -1
      tasks/hisat2.wdl
  3. +29
    -0
      tasks/hisat2_fp.wdl
  4. +1
    -1
      tasks/samtools.wdl
  5. +30
    -30
      workflow.wdl

+ 1
- 1
defaults Прегледај датотеку

@@ -1,5 +1,5 @@
{
"idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
"idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
"gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
"idx_prefix": "genome_snp_tran",
"screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",

+ 1
- 1
tasks/hisat2.wdl Прегледај датотеку

@@ -15,7 +15,7 @@ task hisat2 {
}
runtime {
docker: docker
docker: docker
cluster: cluster
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

+ 29
- 0
tasks/hisat2_fp.wdl Прегледај датотеку

@@ -0,0 +1,29 @@
task hisat2_fp {
File idx
File read_1P
File read_2P
String idx_prefix
String sample_id
String docker
String cluster
String disk_size

command {
nt=$(nproc)
hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${sample_id}.sam --un-conc-gz ${sample_id}_un.fq.gz
}
runtime {
docker: docker
cluster: cluster
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}

output {
File sam=sample_id + ".sam"
File unmapread_1p=sample_id + "_un.fq.1.gz"
File unmapread_2p=sample_id + "_un.fq.2.gz"
}
}

+ 1
- 1
tasks/samtools.wdl Прегледај датотеку

@@ -5,7 +5,7 @@ task samtools {
String sorted_bam=base + ".sorted.bam"
String sorted_bam_index=base + ".sorted.bam.bai"
String samstats=base + ".samstats"
String ins_size=base + ".ins_size"
String ins_size=base + ".ins_size"
String docker
String cluster
String disk_size

+ 30
- 30
workflow.wdl Прегледај датотеку

@@ -2,6 +2,7 @@ import "./tasks/fastqc.wdl" as fastqc
import "./tasks/fastqscreen.wdl" as fastqscreen
import "./tasks/fastp.wdl" as fastp
import "./tasks/qualimap.wdl" as qualimap
import "./tasks/hisat2_fp.wdl" as hisat2_fp
import "./tasks/hisat2.wdl" as hisat2
import "./tasks/samtools.wdl" as samtools
import "./tasks/stringtie.wdl" as stringtie
@@ -43,12 +44,12 @@ workflow {{ project_name }} {
String count_length
String sample_id

Int trim_front1
Int trim_tail1
Int max_len1
Int trim_front2
Int trim_tail2
Int max_len2
Int trim_front1
Int trim_tail1
Int max_len1
Int trim_front2
Int trim_tail2
Int max_len2
Int disable_adapter_trimming
Int length_required
Int umi_len
@@ -63,7 +64,6 @@ workflow {{ project_name }} {
Boolean fastp_run
if (pre_alignment_qc) {
call fastqc.fastqc as fastqc {
input:
read1=read1,
@@ -86,11 +86,10 @@ workflow {{ project_name }} {
}
if (fastp_run){

call fastp.fastp as fastp {
input:
sample_id=sample_id,
read1=read1,
input:
sample_id=sample_id,
read1=read1,
read2=read2,
docker=fastp_docker,
cluster=fastp_cluster,
@@ -99,7 +98,7 @@ workflow {{ project_name }} {
adapter_sequence_r2=adapter_sequence_r2,
umi_loc=umi_loc,
trim_front1=trim_front1,
trim_tail1=trim_tail1,
trim_tail1=trim_tail1,
max_len1=max_len1,
trim_front2=trim_front2,
trim_tail2=trim_tail2,
@@ -113,12 +112,12 @@ workflow {{ project_name }} {
disable_quality_filtering=disable_quality_filtering
}

call hisat2.hisat2 as hisat2 {
input:
sample_id=sample_id,
idx=idx,
idx_prefix=idx_prefix,
read_1P=fastp.Trim_R1,
call hisat2.hisat2_fp as hisat2_fp {
input:
sample_id=sample_id,
idx=idx,
idx_prefix=idx_prefix,
read_1P=fastp.Trim_R1,
read_2P=fastp.Trim_R2,
docker=hisat2_docker,
cluster=hisat2_cluster,
@@ -128,23 +127,24 @@ workflow {{ project_name }} {

if (!fastp_run){
call hisat2.hisat2 as hisat2 {
input:
input:
sample_id=sample_id,
docker=hisat2_docker,
cluster=hisat2_cluster,
idx=idx,
idx_prefix=idx_prefix,
read_1P=read1,
idx=idx,
idx_prefix=idx_prefix,
read_1P=read1,
read_2P=read2,
disk_size=disk_size
}
}
call samtools.samtools as samtools {
input:
input:
docker=samtools_docker,
cluster=samtools_cluster,
sam=hisat2.sam,
insert_size = insert_size,
insert_size=insert_size,
disk_size=disk_size
}

@@ -152,7 +152,7 @@ workflow {{ project_name }} {
call qualimap.qualimap as qualimap {
input:
bam=samtools.out_sort_bam,
gtf=gtf,
gtf=gtf,
docker=qualimap_docker,
cluster=qualimap_cluster,
disk_size=disk_size
@@ -160,25 +160,25 @@ workflow {{ project_name }} {
}

call stringtie.stringtie as stringtie {
input:
input:
docker=stringtie_docker,
cluster=stringtie_cluster,
gtf=gtf,
gtf=gtf,
bam=samtools.out_sort_bam,
disk_size=disk_size
}

call ballgown.ballgown as ballgown {
input:
input:
docker=ballgown_docker,
cluster=ballgown_cluster,
ballgown=stringtie.ballgown,
gene_abundance=stringtie.gene_abundance,
disk_size=disk_size
}
}
call count.count as count {
input:
input:
sample_id=sample_id,
docker=count_docker,
cluster=count_cluster,

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