From dd967de9784d72970913e00ab49c8e58489a2568 Mon Sep 17 00:00:00 2001 From: kevinlibuit Date: Tue, 20 Apr 2021 23:18:06 +0000 Subject: [PATCH] fix formatting --- workflows/wf_ncbi_scrub_pe.wdl | 5 +++-- workflows/wf_ncbi_scrub_se.wdl | 9 +++++---- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/workflows/wf_ncbi_scrub_pe.wdl b/workflows/wf_ncbi_scrub_pe.wdl index 050d197f..b462e5cc 100644 --- a/workflows/wf_ncbi_scrub_pe.wdl +++ b/workflows/wf_ncbi_scrub_pe.wdl @@ -1,6 +1,7 @@ version 1.0 import "../tasks/task_read_clean.wdl" as read_clean +import "../tasks/task_taxonID.wdl" as taxonID workflow dehost_pe { input { @@ -18,7 +19,7 @@ workflow dehost_pe { call taxonID.kraken2 { input: samplename = samplename, - read1 = ncbi_scrub_pe.read1_dehosted + read1 = ncbi_scrub_pe.read1_dehosted, read2 = ncbi_scrub_pe.read2_dehosted } @@ -26,10 +27,10 @@ workflow dehost_pe { File read1_dehosted = ncbi_scrub_pe.read1_dehosted File read2_dehosted = ncbi_scrub_pe.read2_dehosted String ncbi_scrub_docker = ncbi_scrub_pe.ncbi_scrub_docker + Float kraken_human_dehosted = kraken2.percent_human Float kraken_sc2_dehosted = kraken2.percent_sc2 String kraken_report_dehosted = kraken2.kraken_report String kraken_version_dehosted = kraken2.version - String kraken_report_dehosted = kraken2.kraken_report } } diff --git a/workflows/wf_ncbi_scrub_se.wdl b/workflows/wf_ncbi_scrub_se.wdl index 44bb8942..00c03a27 100644 --- a/workflows/wf_ncbi_scrub_se.wdl +++ b/workflows/wf_ncbi_scrub_se.wdl @@ -1,6 +1,7 @@ version 1.0 import "../tasks/task_read_clean.wdl" as read_clean +import "../tasks/task_taxonID.wdl" as taxonID workflow dehost_se { input { @@ -16,14 +17,14 @@ workflow dehost_se { call taxonID.kraken2 { input: samplename = samplename, - read1 = ncbi_scrub_pe.read1_dehosted + read1 = ncbi_scrub_se.read1_dehosted } output { - File reads_dehosted = ncbi_scrub_pe.read1_dehosted - String ncbi_scrub_docker = ncbi_scrub_pe.ncbi_scrub_docker + File reads_dehosted = ncbi_scrub_se.read1_dehosted + String ncbi_scrub_docker = ncbi_scrub_se.ncbi_scrub_docker + Float kraken_human_dehosted = kraken2.percent_human Float kraken_sc2_dehosted = kraken2.percent_sc2 - String kraken_report_dehosted = kraken2.kraken_report String kraken_version_dehosted = kraken2.version String kraken_report_dehosted = kraken2.kraken_report }