From 18424788c042b0ef9e1713fcc200e410729d6b4d Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Thu, 14 May 2020 11:44:30 -0700
Subject: Handle select values on the backend

---
 bh20simplewebuploader/main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 2aebe80..e80713f 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -259,7 +259,7 @@ def parse_input(input_string, html_type, number_step=None):
     Raise NotImplementedError if we forgot to implement a type.
     """
 
-    if html_type == 'text':
+    if html_type == 'text' or html_type == 'select':
         return input_string
     elif html_type == 'number':
         # May be an int or a float.
-- 
cgit v1.2.3


From a259ff7f26458c0810741508df39a4b391ff18d4 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 14 May 2020 16:47:08 -0400
Subject: Workflow fixes

---
 workflows/pangenome-generate/pangenome-generate.cwl | 7 ++++---
 workflows/tools                                     | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index 1d49904..ad8b27f 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -57,8 +57,9 @@ steps:
     in:
       target: dedup/reads_dedup
       query: dedup/reads_dedup
-      outputCIGAR:
-        default: true
+      outputCIGAR: {default: true}
+      preset: {default: asm20}
+      miniWinSize: {default: 1}
     out: [alignments]
     run: ../tools/minimap2/minimap2_paf.cwl
   induceGraph:
@@ -106,7 +107,7 @@ steps:
     out: [ bins, pangenome_sequence ]
   index_paths:
     label: Create path index
-    run : ../tools/odgi/odgi_pathindex.cwl
+    run: ../tools/odgi/odgi_pathindex.cwl
     in:
       sparse_graph_index: buildGraph/odgiGraph
     out: [ indexed_paths ]
diff --git a/workflows/tools b/workflows/tools
index 659e174..1ecbfef 160000
--- a/workflows/tools
+++ b/workflows/tools
@@ -1 +1 @@
-Subproject commit 659e174d0d42ed6b9afd79d9e6f68e225c526d1e
+Subproject commit 1ecbfefa2c064c9b99765a4fb0f84f84e28d35c9
-- 
cgit v1.2.3


From 79a85f846671d575eae6f83d96659c0e1be06011 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 14 May 2020 21:30:19 -0400
Subject: Switch fasta identifiers to use a real working URL

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 bh20seqanalyzer/main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 07e5f69..28b5e31 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -146,7 +146,7 @@ def start_pangenome_analysis(api,
             "class": "File",
             "location": "keep:%s/metadata.yaml" % v["portable_data_hash"]
         })
-        inputobj["subjects"].append("http://arvados.org/keep:%s/sequence.fasta" % v["portable_data_hash"])
+        inputobj["subjects"].append("http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % v["portable_data_hash"])
     run_workflow(api, analysis_project, pangenome_workflow_uuid, "Pangenome analysis", inputobj)
 
 
-- 
cgit v1.2.3