From af48a9707efa76417143f5bb788cee587001a64b Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 28 Jul 2023 14:13:05 +0000
Subject: [PATCH 1/4] perf: update bio/kallisto/index/environment.yaml.

---
 bio/kallisto/index/environment.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bio/kallisto/index/environment.yaml b/bio/kallisto/index/environment.yaml
index 59cf57cc40..feb9c4c6ef 100644
--- a/bio/kallisto/index/environment.yaml
+++ b/bio/kallisto/index/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - kallisto =0.48.0
+  - kallisto =0.50.0

From 0450521f2d8a0ecfcb742e10ff53835b1903179a Mon Sep 17 00:00:00 2001
From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com>
Date: Tue, 1 Aug 2023 10:48:55 +0200
Subject: [PATCH 2/4] Added threads

---
 bio/kallisto/index/wrapper.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/bio/kallisto/index/wrapper.py b/bio/kallisto/index/wrapper.py
index 8dff1139c4..6ccaa29a2a 100644
--- a/bio/kallisto/index/wrapper.py
+++ b/bio/kallisto/index/wrapper.py
@@ -19,9 +19,10 @@
 fasta = " ".join(fasta) if isinstance(fasta, list) else fasta
 
 shell(
-    "kallisto index "  # Tool
-    "{extra} "  # Optional parameters
-    "--index={snakemake.output.index} "  # Output file
-    "{fasta} "  # Input FASTA files
-    "{log}"  # Logging
+    "kallisto index"  # Tool
+    " --threads {snakemake.threads}"
+    " {extra}"  # Optional parameters
+    " --index {snakemake.output.index}"  # Output file
+    " {fasta}"  # Input FASTA files
+    " {log}"  # Logging
 )

From a54d380154c1469466e598f4006320b776146f2f Mon Sep 17 00:00:00 2001
From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com>
Date: Tue, 1 Aug 2023 10:49:52 +0200
Subject: [PATCH 3/4] Fix test file

---
 bio/kallisto/index/test/transcriptome.fasta | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bio/kallisto/index/test/transcriptome.fasta b/bio/kallisto/index/test/transcriptome.fasta
index 11d25dda64..d177d2480b 100644
--- a/bio/kallisto/index/test/transcriptome.fasta
+++ b/bio/kallisto/index/test/transcriptome.fasta
@@ -1,2 +1,2 @@
 >Sheila
-GCTAGCTCAGAAAAAAAAAA
+GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT

From 1a7ebc1919479ff6c585375dd15076acc8f8b2e4 Mon Sep 17 00:00:00 2001
From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com>
Date: Tue, 1 Aug 2023 10:51:27 +0200
Subject: [PATCH 4/4] Update doc

---
 bio/kallisto/index/meta.yaml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/bio/kallisto/index/meta.yaml b/bio/kallisto/index/meta.yaml
index 6cd1e98d57..b48876cae4 100644
--- a/bio/kallisto/index/meta.yaml
+++ b/bio/kallisto/index/meta.yaml
@@ -1,4 +1,11 @@
 name: "kallisto index"
 description: Index a transcriptome using kallisto.
+url: https://github.com/pachterlab/kallisto
 authors:
   - Joël Simoneau
+input:
+  - fasta: FASTA file to index
+output:
+  - index: indexed file
+params:
+  - extra: Additional parameters