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feat: add parameter_meta block to each task
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@mihirsamdarshi
mihirsamdarshi committed Jul 12, 2022
1 parent 5c3da8e commit 7a060ed
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Showing 15 changed files with 198 additions and 27 deletions.
17 changes: 16 additions & 1 deletion wdl/attach_umi/attach_umi.wdl
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Expand Up @@ -2,10 +2,10 @@ version 1.0

task attachUMI {
input {
String SID
File fastqr1
File fastqr2
File fastqi1
String SID

# Runtime Attributes
Int memory
Expand Down Expand Up @@ -41,6 +41,21 @@ task attachUMI {

}

parameter_meta {
SID: {
type: "id"
}
fastqr1: {
label: "Forward End Read FASTQ File"
}
fastqr2: {
type: "Reverse End Read FASTQ File"
}
fastqi1: {
label: "UMI Read FASTQ File"
}
}

meta {
author: "Archana Raja"
}
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11 changes: 11 additions & 0 deletions wdl/bowtie2_align/bowtie2_align.wdl
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Expand Up @@ -47,7 +47,18 @@ task bowtie2_align {
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
}

parameter_meta {
fastqr1: {
label: "Forward End Read FASTQ File"
}
fastqr2: {
type: "Reverse End Read FASTQ File"
}
genome_dir_tar: {
label: "Bowtie2 Reference Tarball File"
}
}

meta {
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14 changes: 7 additions & 7 deletions wdl/collect_qc_metrics/collect_qc.wdl
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Expand Up @@ -60,27 +60,27 @@ task rnaseqQC {
parameter_meta {
SID: {
type: "id"
}
}
trim_summary: {
label: "Trimmed Summary"
label: "CutAdapt Trim Summary Report File"
}
mapped_report: {
label: "Mapped Reads Report"
}
rRNA_report: {
label: "rRNA Report"
label: "Bowtie2 rRNA Sequence Mapping Report"
}
globin_report: {
label: "Globin Report"
label: "Bowtie2 Globin Sequence Mapping Report"
}
phix_report: {
label: "Phix Report"
label: "Bowtie2 Phix Sequence Mapping Report"
}
umi_report: {
label: "UMI Report"
label: "UMI Duplicate Rate Detection Report"
}
star_log: {
label: "STAR Log"
label: "STAR Align Log"
}

}
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14 changes: 13 additions & 1 deletion wdl/collect_rnaseq_metrics/collect_rnaseq_metrics.wdl
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Expand Up @@ -4,9 +4,10 @@ version 1.0
task collectrnaseqmetrics {
input {
String SID
File input_bam
File ref_flat
String SID

Int memory
Int disk_space
Int ncpu
Expand Down Expand Up @@ -44,7 +45,18 @@ task collectrnaseqmetrics {
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
}

parameter_meta {
SID: {
type: "id"
}
input_bam: {
label: "Aligned BAM file"
}
ref_flat: {
label: "RNA Transcript Reference File"
}
}

meta {
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11 changes: 10 additions & 1 deletion wdl/compute_mapped/mapped.wdl
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Expand Up @@ -2,8 +2,9 @@ version 1.0

task samtools_mapped {
input {
File input_bam
String SID
File input_bam

Int memory
Int disk_space
Int ncpu
Expand Down Expand Up @@ -51,7 +52,15 @@ task samtools_mapped {
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
}

parameter_meta {
SID: {
type: "id"
}
input_bam: {
label: "Aligned BAM File"
}
}

meta {
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18 changes: 14 additions & 4 deletions wdl/cutadapt/cutadapt.wdl
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Expand Up @@ -2,12 +2,14 @@ version 1.0

task Cutadapt {
input {
String index_adapter
String univ_adapter
String SID
File fastqr1
File fastqr2
String SID

String index_adapter
String univ_adapter
Int? minimumLength

Int cpus
Int disk_space
Int memory
Expand Down Expand Up @@ -49,11 +51,19 @@ task Cutadapt {
File tooShortPairedOutput = "fastq_trim/tooshort/${SID}_R2.fastq.gz"
}

parameter_meta {
fastqr1: {
label: "Forward End Read FASTQ File"
}
fastqr2: {
type: "Reverse End Read FASTQ File"
}
}

runtime {
docker: "${docker}"
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${cpus}"

}
}
12 changes: 11 additions & 1 deletion wdl/fastqc/fastqc.wdl
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Expand Up @@ -4,7 +4,9 @@ task fastQC {
input {
File fastqr1
File fastqr2

String outdir

Int memory
Int disk_space
Int ncpu
Expand All @@ -30,11 +32,19 @@ task fastQC {
File fastQC_report = '${outdir}.tar.gz'
}

parameter_meta {
fastqr1: {
label: "Forward End Read FASTQ File"
}
fastqr2: {
type: "Reverse End Read FASTQ File"
}
}

runtime {
docker: "${docker}"
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"

}
}
14 changes: 13 additions & 1 deletion wdl/feature_counts/fc.wdl
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Expand Up @@ -4,9 +4,10 @@ version 1.0
task feature_counts {
input {
String SID
File input_bam
File gtf_file
String SID

Int memory
Int disk_space
Int ncpu
Expand Down Expand Up @@ -35,7 +36,18 @@ task feature_counts {
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
}

parameter_meta {
SID: {
type: "id"
}
input_bam: {
label: "Input BAM File"
}
gtf_file: {
label: "GTF-Format Annotation File"
}
}

meta {
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12 changes: 11 additions & 1 deletion wdl/mark_duplicates/mark_duplicates.wdl
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Expand Up @@ -4,8 +4,9 @@ version 1.0
task markduplicates {
input {
File input_bam
String SID
File input_bam

Int memory
Int disk_space
Int ncpu
Expand Down Expand Up @@ -50,6 +51,15 @@ task markduplicates {

}

parameter_meta {
SID: {
type: "ID"
}
input_bam: {
label: "Mapped/Aligned Reads BAM File"
}
}

meta {
author: "Archana Raja"
}
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12 changes: 12 additions & 0 deletions wdl/merge_results/merge_results.wdl
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Expand Up @@ -45,6 +45,18 @@ task merge_results {
File qc_report = "${output_report_name}.csv"
}

parameter_meta {
rsem_files: {
label: "RSEM Gene Count Files"
}
feature_counts_files: {
label: "Feature Counts Files"
}
qc_report_files: {
label: "QC Report Files"
}
}

runtime {
docker: "${docker}"
memory: "${memory}GB"
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12 changes: 11 additions & 1 deletion wdl/multiqc/multiqc.wdl
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Expand Up @@ -3,12 +3,13 @@ version 1.0
task multiQC {
input {
Array[File] fastQCReports
File trim_report

Int memory
Int disk_space
Int ncpu

String docker
File trim_report
}

command <<<
Expand Down Expand Up @@ -52,4 +53,13 @@ task multiQC {
cpu: "${ncpu}"

}

parameter_meta {
fastQCReports: {
label: "FastQC reports"
}
trim_report: {
label: "Trim report"
}
}
}
34 changes: 29 additions & 5 deletions wdl/multiqc/multiqc_postalign.wdl
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Expand Up @@ -4,18 +4,19 @@ version 1.0
task multiQC_postalign {
input {
Int memory
Int disk_space
Int ncpu

String docker
Array[File] fastQCReport
File trim_report
File rsem_report
File star_report
File fc_report
File md_report
File rnametric_report

Int memory
Int disk_space
Int ncpu

String docker
}

command <<<
Expand Down Expand Up @@ -64,6 +65,29 @@ task multiQC_postalign {
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
}

parameter_meta {
fastQCReport: {
label: "FastQC Report Tarball"
}
trim_report: {
label: "CutAdapt Report File"
}
rsem_report: {
label: "RSEM Report File"
}
star_report: {
label: "STAR Align Report File"
}
fc_report: {
label: "FeatureCounts Report File"
}
md_report: {
label: "Picard MarkDuplicates Report File"
}
rnametric_report: {
label: "Picard CollectRnaSeqMetrics Report File"
}
}
}
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