clarify workflow inputs

theiagen · Sep 14, 2021 · 720f628 · 720f628
1 parent dda318e
commit 720f628
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Showing 5 changed files with 30 additions and 30 deletions.
diff --git a/workflows/wf_titan_clearlabs.wdl b/workflows/wf_titan_clearlabs.wdl
@@ -19,9 +19,9 @@ workflow titan_clearlabs {
     String  seq_method  = "ONT via Clear Labs WGS"
     File    primer_bed
     Int?    normalise  = 20000
-    String  dataset_name = "sars-cov-2"
-    String  dataset_reference = "MN908947"
-    String  dataset_tag = "2021-06-25T00:00:00Z"
+    String  nextclade_dataset_name = "sars-cov-2"
+    String  nextclade_dataset_reference = "MN908947"
+    String  nextclade_dataset_tag = "2021-06-25T00:00:00Z"
   }
   call qc_utils.fastqc_se as fastqc_se_raw {
     input:
@@ -75,9 +75,9 @@ workflow titan_clearlabs {
   call taxon_ID.nextclade_one_sample {
     input:
       genome_fasta = consensus.consensus_seq,
-      dataset_name = dataset_name,
-      dataset_reference = dataset_reference,
-      dataset_tag = dataset_tag
+      dataset_name = nextclade_dataset_name,
+      dataset_reference = nextclade_dataset_reference,
+      dataset_tag = nextclade_dataset_tag
   }
   call taxon_ID.nextclade_output_parser_one_sample {
     input:

diff --git a/workflows/wf_titan_fasta.wdl b/workflows/wf_titan_fasta.wdl
@@ -18,9 +18,9 @@ workflow titan_clearlabs {
     File    assembly_fasta
     String  seq_method  
     String  input_assembly_method
-    String  dataset_name = "sars-cov-2"
-    String  dataset_reference = "MN908947"
-    String  dataset_tag = "2021-06-25T00:00:00Z"
+    String  nextclade_dataset_name = "sars-cov-2"
+    String  nextclade_dataset_reference = "MN908947"
+    String  nextclade_dataset_tag = "2021-06-25T00:00:00Z"
   }
   call qc_utils.consensus_qc {
     input:
@@ -34,9 +34,9 @@ workflow titan_clearlabs {
   call taxon_ID.nextclade_one_sample {
     input:
       genome_fasta = assembly_fasta,
-      dataset_name = dataset_name,
-      dataset_reference = dataset_reference,
-      dataset_tag = dataset_tag
+      dataset_name = nextclade_dataset_name,
+      dataset_reference = nextclade_dataset_reference,
+      dataset_tag = nextclade_dataset_tag
   }
   call taxon_ID.nextclade_output_parser_one_sample {
     input:

diff --git a/workflows/wf_titan_illumina_pe.wdl b/workflows/wf_titan_illumina_pe.wdl
@@ -20,9 +20,9 @@ workflow titan_illumina_pe {
     File    read1_raw
     File    read2_raw
     File    primer_bed
-    String  dataset_name = "sars-cov-2"
-    String  dataset_reference = "MN908947"
-    String  dataset_tag = "2021-06-25T00:00:00Z"
+    String  nextclade_dataset_name = "sars-cov-2"
+    String  nextclade_dataset_reference = "MN908947"
+    String  nextclade_dataset_tag = "2021-06-25T00:00:00Z"
 
   }
 
@@ -76,9 +76,9 @@ workflow titan_illumina_pe {
   call taxon_ID.nextclade_one_sample {
     input:
       genome_fasta = consensus.consensus_seq,
-      dataset_name = dataset_name,
-      dataset_reference = dataset_reference,
-      dataset_tag = dataset_tag
+      dataset_name = nextclade_dataset_name,
+      dataset_reference = nextclade_dataset_reference,
+      dataset_tag = nextclade_dataset_tag
   }
   call taxon_ID.nextclade_output_parser_one_sample {
     input:

diff --git a/workflows/wf_titan_illumina_se.wdl b/workflows/wf_titan_illumina_se.wdl
@@ -19,9 +19,9 @@ workflow titan_illumina_se {
     String  seq_method="Illumina single-end"
     File    read1_raw
     File    primer_bed
-    String  dataset_name = "sars-cov-2"
-    String  dataset_reference = "MN908947"
-    String  dataset_tag = "2021-06-25T00:00:00Z"
+    String  nextclade_dataset_name = "sars-cov-2"
+    String  nextclade_dataset_reference = "MN908947"
+    String  nextclade_dataset_tag = "2021-06-25T00:00:00Z"
 
   }
 
@@ -73,9 +73,9 @@ workflow titan_illumina_se {
   call taxon_ID.nextclade_one_sample {
     input:
       genome_fasta = consensus.consensus_seq,
-      dataset_name = dataset_name,
-      dataset_reference = dataset_reference,
-      dataset_tag = dataset_tag
+      dataset_name = nextclade_dataset_name,
+      dataset_reference = nextclade_dataset_reference,
+      dataset_tag = nextclade_dataset_tag
   }
   call taxon_ID.nextclade_output_parser_one_sample {
     input:

diff --git a/workflows/wf_titan_ont.wdl b/workflows/wf_titan_ont.wdl
@@ -19,9 +19,9 @@ workflow titan_ont {
     File   primer_bed
     File   demultiplexed_reads
     Int?   normalise = 200
-    String  dataset_name = "sars-cov-2"
-    String  dataset_reference = "MN908947"
-    String  dataset_tag = "2021-06-25T00:00:00Z"
+    String  nextclade_dataset_name = "sars-cov-2"
+    String  nextclade_dataset_reference = "MN908947"
+    String  nextclade_dataset_tag = "2021-06-25T00:00:00Z"
 
   }
   call qc_utils.fastqc_se as fastqc_se_raw {
@@ -81,9 +81,9 @@ workflow titan_ont {
   call taxon_ID.nextclade_one_sample {
     input:
       genome_fasta = consensus.consensus_seq,
-      dataset_name = dataset_name,
-      dataset_reference = dataset_reference,
-      dataset_tag = dataset_tag
+      dataset_name = nextclade_dataset_name,
+      dataset_reference = nextclade_dataset_reference,
+      dataset_tag = nextclade_dataset_tag
   }
   call taxon_ID.nextclade_output_parser_one_sample {
     input: