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-rw-r--r--workflows/pangenome-generate/pangenome-generate_spoa.cwl5
-rw-r--r--workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl5
2 files changed, 8 insertions, 2 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
index a46524a..4e7302d 100644
--- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl
+++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
@@ -15,6 +15,9 @@ inputs:
type: int
default: 100
doc: Cells per file on component_segmentation
+ reversed_sort:
+ type: string
+ default: "true"
outputs:
odgiGraph:
type: File
@@ -42,7 +45,7 @@ outputs:
# outputSource: segment_components/colinear_components
steps:
dedup_and_sort_by_quality_and_len:
- in: {readsFA: seqs, reversed_sorting: 'true'}
+ in: {readsFA: seqs, reversed_sorting: reversed_sort}
out: [sortedReadsFA, dups]
run: sort_fasta_by_quality_and_len.cwl
induceGraph:
diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
index f8df786..6f71d92 100644
--- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
@@ -1,3 +1,4 @@
+
cwlVersion: v1.1
class: CommandLineTool
hints:
@@ -5,7 +6,8 @@ hints:
coresMin: 1
ramMin: 3000
inputs:
- reversed_sorting:
+ reversed_sorting:
+ type: string
inputBinding: {position: 3}
readsFA:
type: File
@@ -25,3 +27,4 @@ requirements:
InlineJavascriptRequirement: {}
ShellCommandRequirement: {}
baseCommand: [python]
+