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chore: point to this release
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@a-frantz
a-frantz committed Jun 9, 2021
1 parent bc6887d commit 090c838
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Showing 5 changed files with 29 additions and 29 deletions.
4 changes: 2 additions & 2 deletions workflows/general/bwa-db-build.wdl
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version 1.0

import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/bwa.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/util.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/bwa.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/util.wdl"

workflow bwa_db_build {
input {
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20 changes: 10 additions & 10 deletions workflows/qc/quality-check-standard.wdl
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version 1.0

import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/md5sum.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/picard.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/samtools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fastqc.wdl" as fqc
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/ngsderive.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/qualimap.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fastq_screen.wdl" as fq_screen
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/sequencerr.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/multiqc.wdl" as mqc
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/md5sum.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/picard.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/samtools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/fastqc.wdl" as fqc
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/ngsderive.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/qualimap.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/fq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/fastq_screen.wdl" as fq_screen
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/sequencerr.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/multiqc.wdl" as mqc

workflow quality_check {
input {
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14 changes: 7 additions & 7 deletions workflows/rnaseq/rnaseq-standard-fastq.wdl
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version 1.0

import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/fq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/star.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/picard.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/ngsderive.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/htseq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/samtools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/deeptools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/fq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/star.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/picard.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/ngsderive.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/htseq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/samtools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/deeptools.wdl"
import "https://raw.githubusercontent.com/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl" as xenocp_workflow

workflow rnaseq_standard_fastq {
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16 changes: 8 additions & 8 deletions workflows/rnaseq/rnaseq-standard.wdl
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version 1.0

import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/workflows/general/bam-to-fastqs.wdl" as b2fq
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/star.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/picard.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/ngsderive.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/htseq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/samtools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/util.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/deeptools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/workflows/general/bam-to-fastqs.wdl" as b2fq
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/star.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/picard.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/ngsderive.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/htseq.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/samtools.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/util.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/deeptools.wdl"
import "https://raw.githubusercontent.com/stjude/xenocp/3.1.1/wdl/workflows/xenocp.wdl" as xenocp_workflow

workflow rnaseq_standard {
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4 changes: 2 additions & 2 deletions workflows/rnaseq/rnaseq-star-db-build.wdl
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version 1.0

import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/star.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.0/tools/util.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/star.wdl"
import "https://raw.githubusercontent.com/stjudecloud/workflows/quality-check-standard/v1.0.1/tools/util.wdl"

workflow rnaseq_star_db_build {
input {
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