From 00832a26c59cbfcc16f7142c1f809b70613d4b47 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Wed, 3 Jun 2020 20:39:33 -0400 Subject: [PATCH] filter_subsample_sequences should emit input/output sequence counts --- pipes/WDL/tasks/tasks_nextstrain.wdl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 52c3fe5cd..e38348387 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -123,6 +123,8 @@ task filter_subsample_sequences { ~{"--exclude-where " + exclude_where} \ ~{"--include-where " + include_where} \ --output "~{in_basename}.filtered.fasta" + cat ~{sequences_fasta} | grep \> | wc -l > IN_COUNT + cat ~{in_basename}.filtered.fasta | grep \> | wc -l > OUT_COUNT } runtime { docker: docker @@ -133,8 +135,10 @@ task filter_subsample_sequences { preemptible: 1 } output { - File filtered_fasta = "~{in_basename}.filtered.fasta" - String augur_version = read_string("VERSION") + File filtered_fasta = "~{in_basename}.filtered.fasta" + String augur_version = read_string("VERSION") + Int sequences_in = read_int("IN_COUNT") + Int sequences_out = read_int("OUT_COUNT") } }