From 3c35250eb6394ec8d0e28e4391ec23f2223345c8 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 21 Nov 2020 21:21:36 +0100
Subject: generalized spoa workflow

---
 workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl')

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 26c20e8..f8df786 100644
--- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
@@ -5,6 +5,8 @@ hints:
     coresMin: 1
     ramMin: 3000
 inputs:
+    reversed_sorting:
+    inputBinding: {position: 3}
   readsFA:
     type: File
     inputBinding: {position: 2}
-- 
cgit v1.2.3


From 862ae0235e3d1b105fa342cedf4aa59ae73d90c4 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 21 Nov 2020 22:00:34 +0100
Subject: added reversed_sorting parameter; typos

---
 workflows/pangenome-generate/pangenome-generate_spoa.cwl       | 5 ++++-
 workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

(limited to 'workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl')

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]
+
-- 
cgit v1.2.3