From 9aa16ba38dbc396856e25d440b6e8cb11bf27e7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?In=C3=AAs=20Mendes?= Date: Thu, 14 Sep 2023 19:00:46 +0100 Subject: [PATCH] Patch theiaprok ont - change est_genome_size to Int (#179) * change est_genome_size to Int * change est_genome_size to INT --- tasks/utilities/task_kmc.wdl | 2 +- workflows/theiaprok/wf_theiaprok_ont.wdl | 2 +- workflows/utilities/wf_read_QC_trim_ont.wdl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tasks/utilities/task_kmc.wdl b/tasks/utilities/task_kmc.wdl index a8f32be4e..4d62c85a6 100644 --- a/tasks/utilities/task_kmc.wdl +++ b/tasks/utilities/task_kmc.wdl @@ -44,7 +44,7 @@ task kmc { tail -n8 LOG > ~{samplename}_kmer_stats.txt >>> output { - String est_genome_size = read_string("UNIQUE_COUNTED") + Int est_genome_size = read_int("UNIQUE_COUNTED") File kmer_stats = "~{samplename}_kmer_stats.txt" String kmc_version = read_string("VERSION") } diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl index 06628be0a..6057ddce0 100644 --- a/workflows/theiaprok/wf_theiaprok_ont.wdl +++ b/workflows/theiaprok/wf_theiaprok_ont.wdl @@ -489,7 +489,7 @@ workflow theiaprok_ont { String? nanoplot_version = nanoplot_raw.nanoplot_version String? nanoplot_docker = nanoplot_raw.nanoplot_docker # Read QC - kmc outputs - String? kmc_est_genome_size = read_qc_trim.est_genome_size + Int? kmc_est_genome_size = read_qc_trim.est_genome_size File? kmc_kmer_stats = read_qc_trim.kmc_kmer_stats String? kmc_version = read_qc_trim.kmc_version # Read QC - rasusa outputs diff --git a/workflows/utilities/wf_read_QC_trim_ont.wdl b/workflows/utilities/wf_read_QC_trim_ont.wdl index 779d479c0..c0f361c84 100644 --- a/workflows/utilities/wf_read_QC_trim_ont.wdl +++ b/workflows/utilities/wf_read_QC_trim_ont.wdl @@ -84,7 +84,7 @@ workflow read_QC_trim_ont { } output { # kmc outputs - String est_genome_size = kmc.est_genome_size + Int est_genome_size = kmc.est_genome_size File kmc_kmer_stats = kmc.kmer_stats String kmc_version = kmc.kmc_version