Browse Source

Remove sample_id.

tags/v0.2.0
YJC 4 years ago
parent
commit
d679a3bdeb
7 changed files with 8 additions and 15 deletions
  1. +1
    -1
      tasks/ballgown.wdl
  2. +2
    -1
      tasks/count.wdl
  3. +1
    -1
      tasks/fastp.wdl
  4. +1
    -1
      tasks/hisat2.wdl
  5. +1
    -1
      tasks/samtools.wdl
  6. +1
    -1
      tasks/stringtie.wdl
  7. +1
    -9
      workflow.wdl

+ 1
- 1
tasks/ballgown.wdl View File

task ballgown { task ballgown {
File gene_abundance File gene_abundance
Array[File] ballgown Array[File] ballgown
String sample_id
String sample_id=basename(gene_abundance, ".gene.abundance.txt")
String docker String docker
String cluster String cluster
String disk_size String disk_size

+ 2
- 1
tasks/count.wdl View File

task count { task count {
File gene_abundance
Array[File] ballgown Array[File] ballgown
String sample_id
String sample_id=basename(gene_abundance, ".gene.abundance.txt")
String docker String docker
String cluster String cluster
String disk_size String disk_size

+ 1
- 1
tasks/fastp.wdl View File

task fastp { task fastp {
String sample_id
File read1 File read1
File read2 File read2
String sample_id=sub(basename(read1), "_R1\\.(fastq|fq)\\.gz$", "")
String adapter_sequence String adapter_sequence
String adapter_sequence_r2 String adapter_sequence_r2
String docker String docker

+ 1
- 1
tasks/hisat2.wdl View File

File Trim_R1 File Trim_R1
File Trim_R2 File Trim_R2
String idx_prefix String idx_prefix
String sample_id
String sample_id=basename(Trim_R1, "_R1.fastq.gz")
String docker String docker
String cluster String cluster
String disk_size String disk_size

+ 1
- 1
tasks/samtools.wdl View File

task samtools { task samtools {
File sam File sam
String sample_id
String sample_id=basename(sam, ".sam")
String bam = sample_id + ".bam" String bam = sample_id + ".bam"
String sorted_bam = sample_id + ".sorted.bam" String sorted_bam = sample_id + ".sorted.bam"
String percent_bam = sample_id + ".percent.bam" String percent_bam = sample_id + ".percent.bam"

+ 1
- 1
tasks/stringtie.wdl View File

File bam File bam
File gtf File gtf
String docker String docker
String sample_id
String sample_id=basename(bam, ".sorted.bam")
String cluster String cluster
String disk_size String disk_size
Int minimum_length_allowed_for_the_predicted_transcripts Int minimum_length_allowed_for_the_predicted_transcripts

+ 1
- 9
workflow.wdl View File

import "./tasks/ballgown.wdl" as ballgown import "./tasks/ballgown.wdl" as ballgown
import "./tasks/count.wdl" as count import "./tasks/count.wdl" as count



workflow {{ project_name }} { workflow {{ project_name }} {
File read1 File read1
File read2 File read2
File screen_ref_dir File screen_ref_dir
File fastq_screen_conf File fastq_screen_conf
File gtf File gtf
String sample_id
String fastp_docker String fastp_docker
String adapter_sequence String adapter_sequence
String adapter_sequence_r2 String adapter_sequence_r2


call fastp.fastp as fastp { call fastp.fastp as fastp {
input: input:
sample_id=sample_id,
read1 = read1, read1 = read1,
read2 = read2, read2 = read2,
docker = fastp_docker, docker = fastp_docker,
qualified_quality_phred = qualified_quality_phred, qualified_quality_phred = qualified_quality_phred,
length_required1 = length_required1, length_required1 = length_required1,
disable_quality_filtering = disable_quality_filtering disable_quality_filtering = disable_quality_filtering
}
}


call fastqc.fastqc as fastqc { call fastqc.fastqc as fastqc {
input: input:


call hisat2.hisat2 as hisat2 { call hisat2.hisat2 as hisat2 {
input: input:
sample_id = sample_id,
idx = idx, idx = idx,
idx_prefix = idx_prefix, idx_prefix = idx_prefix,
Trim_R1 = fastp.Trim_R1, Trim_R1 = fastp.Trim_R1,


call samtools.samtools as samtools { call samtools.samtools as samtools {
input: input:
sample_id = sample_id,
sam = hisat2.sam, sam = hisat2.sam,
docker = samtools_docker, docker = samtools_docker,
cluster = samtools_cluster, cluster = samtools_cluster,


call stringtie.stringtie as stringtie { call stringtie.stringtie as stringtie {
input: input:
sample_id = sample_id,
gtf = gtf, gtf = gtf,
bam = samtools.out_bam, bam = samtools.out_bam,
docker = stringtie_docker, docker = stringtie_docker,


call ballgown.ballgown as ballgown { call ballgown.ballgown as ballgown {
input: input:
sample_id = sample_id,
docker = ballgown_docker, docker = ballgown_docker,
cluster = ballgown_cluster, cluster = ballgown_cluster,
ballgown = stringtie.ballgown, ballgown = stringtie.ballgown,


call count.count as count { call count.count as count {
input: input:
sample_id = sample_id,
docker = count_docker, docker = count_docker,
cluster = count_cluster, cluster = count_cluster,
ballgown = stringtie.ballgown, ballgown = stringtie.ballgown,

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