From 2f09de3653daac517deafa00b3f7f12e6493e59b Mon Sep 17 00:00:00 2001
From: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com>
Date: Wed, 15 May 2024 08:24:11 -0400
Subject: [PATCH] Np fix paired tag (#1279)

* rename some intermediate inputs for paired tag demultiplexing

* rename some intermediate inputs for paired tag demultiplexing

* changelogs

* changelogs

* changelogs again

* changelogs again

* changelogs again
---
 pipelines/skylab/multiome/Multiome.changelog.md    | 5 +++++
 pipelines/skylab/multiome/Multiome.wdl             | 3 +--
 pipelines/skylab/multiome/atac.changelog.md        | 5 +++++
 pipelines/skylab/multiome/atac.wdl                 | 3 ++-
 pipelines/skylab/paired_tag/PairedTag.changelog.md | 5 +++++
 pipelines/skylab/paired_tag/PairedTag.wdl          | 2 +-
 tasks/skylab/PairedTagUtils.wdl                    | 6 +++---
 7 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
index 31d1b391d7..f0b69bdcd5 100644
--- a/pipelines/skylab/multiome/Multiome.changelog.md
+++ b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,8 @@
+# 3.4.5
+2024-05-14 (Date of Last Commit)
+
+* Updated the Paired-tag Demultiplex task so that some intermediate input names have been renamed; this change does not impact the Multiome workflow
+
 # 3.4.4
 2024-05-10 (Date of Last Commit)
 
diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
index cfc5ef3d23..526381b707 100644
--- a/pipelines/skylab/multiome/Multiome.wdl
+++ b/pipelines/skylab/multiome/Multiome.wdl
@@ -7,7 +7,7 @@ import "https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.0/wdl/c
 
 workflow Multiome {
 
-    String pipeline_version = "3.4.4"
+    String pipeline_version = "3.4.5"
 
     input {
         String input_id
@@ -47,7 +47,6 @@ workflow Multiome {
 
         # CellBender
         Boolean run_cellbender = false
-
     }
 
     # Call the Optimus workflow
diff --git a/pipelines/skylab/multiome/atac.changelog.md b/pipelines/skylab/multiome/atac.changelog.md
index 693172fefc..54948b799f 100644
--- a/pipelines/skylab/multiome/atac.changelog.md
+++ b/pipelines/skylab/multiome/atac.changelog.md
@@ -1,3 +1,8 @@
+# 1.2.3
+2024-05-14 (Date of Last Commit)
+
+* Updated the demultiplex task so that some intermediate input names have been renamed, this does not impact the ATAC workflow
+
 # 1.2.2
 2024-05-10 (Date of Last Commit)
 
diff --git a/pipelines/skylab/multiome/atac.wdl b/pipelines/skylab/multiome/atac.wdl
index a06cbd45ac..e8fa467264 100644
--- a/pipelines/skylab/multiome/atac.wdl
+++ b/pipelines/skylab/multiome/atac.wdl
@@ -41,7 +41,7 @@ workflow ATAC {
     String adapter_seq_read3 = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG"
   }
 
-  String pipeline_version = "1.2.2"
+  String pipeline_version = "1.2.3"
 
   parameter_meta {
     read1_fastq_gzipped: "read 1 FASTQ file as input for the pipeline, contains read 1 of paired reads"
@@ -118,6 +118,7 @@ workflow ATAC {
 
     }
   }
+
   File bam_aligned_output_atac = select_first([BBTag.bb_bam, BWAPairedEndAlignment.bam_aligned_output])
   File fragment_file_atac = select_first([BB_fragment.fragment_file, CreateFragmentFile.fragment_file])
   File snap_metrics_atac = select_first([BB_fragment.Snap_metrics,CreateFragmentFile.Snap_metrics])
diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md
index ef69a9376a..e7c4f9b23f 100644
--- a/pipelines/skylab/paired_tag/PairedTag.changelog.md
+++ b/pipelines/skylab/paired_tag/PairedTag.changelog.md
@@ -1,3 +1,8 @@
+# 0.6.1
+2024-05-14 (Date)
+
+* Updated the demultiplex task so that some intermediate input names have been renamed. There is no change to the outputs.
+
 # 0.6.0
 2024-05-10 (Date)
 
diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl
index c05df55b94..83756fbc4c 100644
--- a/pipelines/skylab/paired_tag/PairedTag.wdl
+++ b/pipelines/skylab/paired_tag/PairedTag.wdl
@@ -5,7 +5,7 @@ import "../../../pipelines/skylab/optimus/Optimus.wdl" as optimus
 import "../../../tasks/skylab/H5adUtils.wdl" as H5adUtils
 import "../../../tasks/skylab/PairedTagUtils.wdl" as Demultiplexing
 workflow PairedTag {
-    String pipeline_version = "0.6.0"
+    String pipeline_version = "0.6.1"
 
     input {
         String input_id
diff --git a/tasks/skylab/PairedTagUtils.wdl b/tasks/skylab/PairedTagUtils.wdl
index a34b3c3187..ca5b6cf885 100644
--- a/tasks/skylab/PairedTagUtils.wdl
+++ b/tasks/skylab/PairedTagUtils.wdl
@@ -106,9 +106,9 @@ task PairedTagDemultiplex {
         elif [[ $COUNT == 24 && ~{preindex} == "false" ]]
           then
           echo "FASTQ has correct index length, no modification necessary"
-          mv "~{input_id}_R2_prefix.fq.gz" "~{r2_base}.fq.gz"
-          mv "~{input_id}_R1_prefix.fq.gz" "~{r1_base}.fq.gz"
-          mv "~{input_id}_R3_prefix.fq.gz" "~{r3_base}.fq.gz"
+          mv "~{input_id}_R2.fq.gz" "~{r2_base}.fq.gz"
+          mv "~{input_id}_R1.fq.gz" "~{r1_base}.fq.gz"
+          mv "~{input_id}_R3.fq.gz" "~{r3_base}.fq.gz"
         elif [[ $COUNT == 24 && ~{preindex} == "true" ]]
           then
           pass="false"