update output docs

theiagen · Nov 15, 2024 · eedfd54 · eedfd54
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diff --git a/docs/workflows/standalone/dorado_basecalling.md b/docs/workflows/standalone/dorado_basecalling.md
@@ -101,10 +101,13 @@ This workflow is composed of several tasks to process, basecall, and analyze rab
 
 | **Variable** | **Type** | **Description** |
 |---|---|---|
-| **basecalled_fastqs** | Array[File] | Array of FASTQ files generated from basecalling |
-| **demuxed_fastqs** | Array[File] | FASTQ files produced from BAM demultiplexing |
-| **logs** | Array[File] | Log files from the demultiplexing process |
+| **fastq_files** | Array[File] | FASTQ files produced from basecalling and demultiplexing |
 | **terra_table_tsv** | File | TSV file for Terra table upload |
+| **dorado_version** | String | Version of Dorado used in the workflow |
+| **dorado_model** | String | Model used for basecalling |
+|  **samtools_version** | String | Version of Samtools used in the workflow |
+|  **dorado_analysis_date** | String | Date of Dorado analysis |
+|  **dorado_phb_version** | String | Version of Dorado PHB workflow |
 
 ## References
 <!-- -->

diff --git a/tasks/basecalling/task_dorado_demux.wdl b/tasks/basecalling/task_dorado_demux.wdl
@@ -16,8 +16,7 @@ task dorado_demux {
     set -euo pipefail
 
     # Capture Dorado version
-    dorado --version 2>&1 | tee DORADO_VERSION
-    echo "Dorado version:" $(cat DORADO_VERSION)
+    dorado --version 2>&1 | head -n1 | tee DORADO_VERSION
 
     # Output the Dorado model used
     echo "~{dorado_model_used}" > DORADO_MODEL_USED

diff --git a/tasks/basecalling/task_samtools_convert.wdl b/tasks/basecalling/task_samtools_convert.wdl
@@ -13,7 +13,7 @@ task samtools_convert {
     set -euo pipefail
 
     # samtools version
-    samtools --version | head -n1 | tee VERSION
+    samtools --version | head -n1 | tee SAMTOOLS_VERSION
 
     bam_output="output/bam/"
     mkdir -p "$bam_output"