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chore: bump to v3.0.1
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-45
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‎workflows/general/bam-to-fastqs.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/fq.wdl"
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workflow bam_to_fastqs {
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input {

‎workflows/general/bwa-db-build.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/bwa.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/wget.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/bwa.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/wget.wdl"
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workflow bwa_db_build {
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input {

‎workflows/qc/make-qc-reference.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fastq_screen.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/fastq_screen.wdl"
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workflow make_qc_reference {
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call fastq_screen.build_db as fastq_screen_build_db

‎workflows/qc/quality-check-standard.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/md5sum.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fastqc.wdl" as fqc
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/qualimap.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fastq_screen.wdl" as fq_screen
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/multiqc.wdl" as mqc
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/md5sum.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/fastqc.wdl" as fqc
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/qualimap.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/fq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/fastq_screen.wdl" as fq_screen
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/multiqc.wdl" as mqc
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workflow quality_check {
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input {

‎workflows/rnaseq/ESTIMATE.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/estimate.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/estimate.wdl"
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workflow ESTIMATE {
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input {

‎workflows/rnaseq/calc-gene-lengths.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/util.wdl"
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workflow calc_gene_lengths {
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input {

‎workflows/rnaseq/rnaseq-standard-fastq.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/fq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/star.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/htseq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/deeptools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/fq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/star.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/htseq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/deeptools.wdl"
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import "https://raw.githubusercontent.com/stjude/xenocp/3.1.4/wdl/workflows/xenocp.wdl"
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workflow rnaseq_standard_fastq {

‎workflows/rnaseq/rnaseq-standard.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/workflows/general/bam-to-fastqs.wdl" as b2fq
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/star.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/htseq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/deeptools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/workflows/general/bam-to-fastqs.wdl" as b2fq
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/star.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/picard.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/htseq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/deeptools.wdl"
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import "https://raw.githubusercontent.com/stjude/xenocp/3.1.4/wdl/workflows/xenocp.wdl"
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workflow rnaseq_standard {

‎workflows/rnaseq/rnaseq-star-db-build.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/star.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/wget.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/star.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/wget.wdl"
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workflow rnaseq_star_db_build {
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input {

‎workflows/rnaseq_expression_classification/rnaseq_expression_classification.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/workflows/rnaseq/rnaseq-standard.wdl" as rnav2
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/tsne.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/workflows/rnaseq/rnaseq-standard.wdl" as rnav2
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/tsne.wdl"
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workflow rnaseq_expression_classification {
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input {

‎workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_bams.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/htseq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/tsne.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/htseq.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/samtools.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/ngsderive.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/tsne.wdl"
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workflow rnaseq_expression_classification_from_bams {
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input {

‎workflows/rnaseq_expression_classification/rnaseq_expression_classification_from_counts.wdl

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version 1.0
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/tsne.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/util.wdl"
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import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.1/tools/tsne.wdl"
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workflow rnaseq_expression_classification_from_counts {
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input {

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