From 99487d108df8089d4ac9008ab64b92919641dea7 Mon Sep 17 00:00:00 2001 From: Lydia Andreyevna Krasilnikova Date: Sun, 14 Jul 2024 09:14:04 -0400 Subject: [PATCH] added workflow --- .../workflows/fetch_sra_to_bam_bam_only.wdl | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/pipes/WDL/workflows/fetch_sra_to_bam_bam_only.wdl b/pipes/WDL/workflows/fetch_sra_to_bam_bam_only.wdl index 8b1378917..922f99589 100644 --- a/pipes/WDL/workflows/fetch_sra_to_bam_bam_only.wdl +++ b/pipes/WDL/workflows/fetch_sra_to_bam_bam_only.wdl @@ -1 +1,27 @@ + + +workflow fetch_sra_to_bam_bam_only { + meta { + description: "Retrieve reads from the NCBI Short Read Archive in unaligned BAM format." + author: "Broad Viral Genomics" + email: "viral-ngs@broadinstitute.org" + allowNestedInputs: true + } + + call terra.check_terra_env + + #if(check_terra_env.is_running_on_terra) { + call ncbi_tools.Fetch_SRA_to_BAM_BAM_only { + input: + email_address = select_first([check_terra_env.user_email, ""]) + } + #} + #if(!check_terra_env.is_running_on_terra) { + # call ncbi_tools.Fetch_SRA_to_BAM + #} + + output { + File reads_ubam = Fetch_SRA_to_BAM_BAM_only.reads_ubam + } +}