From f945a010e2c2bfa6cf2edd39ceabcc85556a40e4 Mon Sep 17 00:00:00 2001
From: lvreynoso <lreynoso@chanzuckerberg.com>
Date: Fri, 18 Aug 2023 15:09:00 -0700
Subject: [PATCH] Use hisat2 task outputs instead of fastp outputs as redup
 input

---
 scripts/release.sh    |  2 +-
 workflows/amr/run.wdl | 10 +++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/scripts/release.sh b/scripts/release.sh
index 832f16df7..92dec7e51 100755
--- a/scripts/release.sh
+++ b/scripts/release.sh
@@ -28,7 +28,7 @@ OLD_TAG=$(git describe --tags --match "${WORKFLOW_NAME}-v*" || echo "${WORKFLOW_
 #     exit 1
 # fi
 
-TAG="amr-v1.3.0-beta.2"
+TAG="amr-v1.3.0-beta.3"
 
 if [[ $( git branch --show-current) != "main" ]]; then 
     COMMIT=$(git rev-parse --short HEAD)
diff --git a/workflows/amr/run.wdl b/workflows/amr/run.wdl
index aad861e65..c5f2e16bd 100644
--- a/workflows/amr/run.wdl
+++ b/workflows/amr/run.wdl
@@ -29,9 +29,13 @@ workflow amr {
             docker_image_id = host_filtering_docker_image_id,
             s3_wd_uri = s3_wd_uri
         }
+
+        File hisat2_filtered1_fastq = select_first([host_filter_stage.hisat2_human_filtered1_fastq, host_filter_stage.hisat2_host_filtered1_fastq])
+        File? hisat2_filtered2_fastq = if defined(host_filter_stage.hisat2_human_filtered2_fastq) then host_filter_stage.hisat2_human_filtered2_fastq
+                                                                          else host_filter_stage.hisat2_host_filtered2_fastq
         call RunRedup {
             input:
-            fastp_fa = select_all([host_filter_stage.fastp_out_fastp1_fastq, host_filter_stage.fastp_out_fastp2_fastq]),
+            superset_fqs = select_all([hisat2_filtered1_fastq, hisat2_filtered2_fastq]),
             non_host_reads = select_all(
                 [
                     host_filter_stage.subsampled_out_subsampled_1_fa,
@@ -163,7 +167,7 @@ workflow amr {
 
 task RunRedup {
     input {
-        Array[File] fastp_fa
+        Array[File] superset_fqs
         Array[File] non_host_reads
         File clusters
         File cluster_sizes
@@ -205,7 +209,7 @@ task RunRedup {
         CODE
 
         counter=1
-        for fasta in ~{sep=' ' fastp_fa}; do
+        for fasta in ~{sep=' ' superset_fqs}; do
             seqtk subseq $fasta duplicated-pairs.txt | seqtk seq -a > redups_$counter.fa
             ((counter++))
         done