Merge branch 'develop' into azurized_wdls

broadinstitute · May 15, 2024 · 9cd7ca1 · 9cd7ca1
2 parents ebb3c39 + 2f09de3
commit 9cd7ca1
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diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,7 +1,8 @@
 # 3.4.5
-2024-05-11 (Date of Last Commit)
+2024-05-14 (Date of Last Commit)
 
 * Updated the PairedTag.wdl to run on Azure. This change does not affect the Multiome pipeline.
+* 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
@@ -8,7 +8,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Multiome {
 
-    String pipeline_version = "3.4.4"
+    String pipeline_version = "3.4.5"
 
     input {
         String cloud_provider
@@ -45,7 +45,6 @@ workflow Multiome {
 
         # CellBender
         Boolean run_cellbender = false
-
     }
 
     # Determine docker prefix based on cloud provider

diff --git a/pipelines/skylab/multiome/atac.changelog.md b/pipelines/skylab/multiome/atac.changelog.md
@@ -1,8 +1,9 @@
 # 1.2.3
-2024-05-12 (Date of Last Commit)
+2024-05-14 (Date of Last Commit)
 
-*  Updated the Optimus.wdl to run on Azure. This change does not affect the ATAC pipeline.
-*  Updated the PairedTag.wdl to run on Azure. This change does not affect the ATAC pipeline.
+* Updated the Optimus.wdl to run on Azure. This change does not affect the ATAC pipeline.
+* Updated the PairedTag.wdl to run on Azure. This change does not affect the ATAC pipeline.
+* 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
@@ -68,6 +68,7 @@ workflow ATAC {
 
 
 
+
   parameter_meta {
     read1_fastq_gzipped: "read 1 FASTQ file as input for the pipeline, contains read 1 of paired reads"
     read2_fastq_gzipped: "read 2 FASTQ file as input for the pipeline, contains the cellular barcodes corresponding to the reads in the read1 FASTQ and read 3 FASTQ"
@@ -149,6 +150,7 @@ 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
@@ -1,7 +1,8 @@
 # 0.6.1
-2024-05-12 (Date of Last Commit)
+2024-05-14 (Date of Last Commit)
 
 * Updated the PairedTag.wdl to run in Azure 
+* 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/tasks/skylab/PairedTagUtils.wdl b/tasks/skylab/PairedTagUtils.wdl
@@ -107,7 +107,6 @@ task PairedTagDemultiplex {
         elif [[ $COUNT == 24 && ~{preindex} == "false" ]]
           then
           echo "FASTQ has correct index length, no modification necessary"
-          ls -lh
           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"