From 32684f718a2a5f55be1c764e1fd8f3b89647b3cd Mon Sep 17 00:00:00 2001 From: Brian Haas Date: Tue, 25 Jun 2024 18:35:54 -0400 Subject: [PATCH 1/3] set ctat genome libs to new location at: mdl-ctat-genome-libs/ --- WDL/Terra/ctat_mutations.Terra.hg38.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WDL/Terra/ctat_mutations.Terra.hg38.wdl b/WDL/Terra/ctat_mutations.Terra.hg38.wdl index d208716..301cd3a 100644 --- a/WDL/Terra/ctat_mutations.Terra.hg38.wdl +++ b/WDL/Terra/ctat_mutations.Terra.hg38.wdl @@ -22,7 +22,7 @@ workflow ctat_mutations_Terra_hg38 { Int? preemptible - String gs_base_url = "gs://ctat_genome_libs/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play" + String gs_base_url = "gs://mdl-ctat-genome-libs/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play" Ctat_mutations_config pipe_inputs_config = { From 85b58d3612a094e8299071ac5b832a77c00a9546 Mon Sep 17 00:00:00 2001 From: Brian Haas Date: Tue, 25 Jun 2024 18:36:21 -0400 Subject: [PATCH 2/3] set ctat genome libs to new location at: mdl-ctat-genome-libs/ --- WDL/Terra/ctat_mutations.Terra.hg19.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/WDL/Terra/ctat_mutations.Terra.hg19.wdl b/WDL/Terra/ctat_mutations.Terra.hg19.wdl index 6c21087..c276611 100644 --- a/WDL/Terra/ctat_mutations.Terra.hg19.wdl +++ b/WDL/Terra/ctat_mutations.Terra.hg19.wdl @@ -19,7 +19,7 @@ workflow ctat_mutations_Terra_hg19 { Boolean is_long_reads = false Int? preemptible - String gs_base_url = "gs://ctat_genome_libs/__genome_libs_StarFv1.10/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play" + String gs_base_url = "gs://mdl-ctat-genome-libs/__genome_libs_StarFv1.10/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play" Ctat_mutations_config pipe_inputs_config = { "genome_version" : "hg19", From 2c44304035376b53dcdde7a28d5284f52626ae09 Mon Sep 17 00:00:00 2001 From: Brian Haas Date: Sat, 29 Jun 2024 08:58:42 -0400 Subject: [PATCH 3/3] included aligned bai as output --- WDL/Terra/ctat_mutations.Terra.hg19.wdl | 1 + WDL/Terra/ctat_mutations.Terra.hg38.wdl | 1 + WDL/Terra/ctat_mutations.Terra.wdl | 1 + WDL/ctat_mutations.wdl | 1 + 4 files changed, 4 insertions(+) diff --git a/WDL/Terra/ctat_mutations.Terra.hg19.wdl b/WDL/Terra/ctat_mutations.Terra.hg19.wdl index c276611..a2fdfda 100644 --- a/WDL/Terra/ctat_mutations.Terra.hg19.wdl +++ b/WDL/Terra/ctat_mutations.Terra.hg19.wdl @@ -69,6 +69,7 @@ workflow ctat_mutations_Terra_hg19 { File? annotated_vcf = CM_Terra_wf.annotated_vcf File? filtered_vcf = CM_Terra_wf.filtered_vcf File? aligned_bam = CM_Terra_wf.aligned_bam + File? aligned_bai = CM_Terra_wf.aligned_bai File? output_log_final = CM_Terra_wf.output_log_final File? output_SJ = CM_Terra_wf.output_SJ File? recalibrated_bam = CM_Terra_wf.recalibrated_bam diff --git a/WDL/Terra/ctat_mutations.Terra.hg38.wdl b/WDL/Terra/ctat_mutations.Terra.hg38.wdl index 301cd3a..d58bbba 100644 --- a/WDL/Terra/ctat_mutations.Terra.hg38.wdl +++ b/WDL/Terra/ctat_mutations.Terra.hg38.wdl @@ -76,6 +76,7 @@ workflow ctat_mutations_Terra_hg38 { File? annotated_vcf = CM_Terra_wf.annotated_vcf File? filtered_vcf = CM_Terra_wf.filtered_vcf File? aligned_bam = CM_Terra_wf.aligned_bam + File? aligned_bai = CM_Terra_wf.aligned_bai File? output_log_final = CM_Terra_wf.output_log_final File? output_SJ = CM_Terra_wf.output_SJ File? recalibrated_bam = CM_Terra_wf.recalibrated_bam diff --git a/WDL/Terra/ctat_mutations.Terra.wdl b/WDL/Terra/ctat_mutations.Terra.wdl index 67fb752..fcc9632 100644 --- a/WDL/Terra/ctat_mutations.Terra.wdl +++ b/WDL/Terra/ctat_mutations.Terra.wdl @@ -105,6 +105,7 @@ workflow ctat_mutations_Terra { File? annotated_vcf = CM_wf.annotated_vcf File? filtered_vcf = CM_wf.filtered_vcf File? aligned_bam = CM_wf.aligned_bam + File? aligned_bai = CM_wf.aligned_bai File? output_log_final = CM_wf.output_log_final File? output_SJ = CM_wf.output_SJ File? recalibrated_bam = CM_wf.recalibrated_bam diff --git a/WDL/ctat_mutations.wdl b/WDL/ctat_mutations.wdl index df70f11..209a482 100644 --- a/WDL/ctat_mutations.wdl +++ b/WDL/ctat_mutations.wdl @@ -615,6 +615,7 @@ workflow ctat_mutations { File? annotated_vcf = AnnotateVariants.vcf File? filtered_vcf = VariantFiltration.vcf File? aligned_bam = StarAlign.bam + File? aligned_bai = StarAlign.bai File? output_log_final = StarAlign.output_log_final File? output_SJ = StarAlign.output_SJ File? recalibrated_bam = ApplyBQSR.bam