perf: autobump bio/kallisto/quant (#1629)

Automatic update of bio/kallisto/quant.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/kallisto/quant/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - kallisto =0.48.0
+  - kallisto =0.50.0

bio/kallisto/quant/meta.yaml

@@ -1,4 +1,12 @@
 name: "kallisto quant"
 description: Pseudoalign reads and quantify transcripts using kallisto.
+url: https://github.com/pachterlab/kallisto
 authors:
   - Joël Simoneau
+input:
+  - fastq: FASTQ file(s)
+  - index: indexed file
+output:
+  - directory with results
+params:
+  - extra: Additional parameters

bio/kallisto/quant/test/reads/A_R1.fastq

@@ -1,4 +1,4 @@
 @1
-GCTAGC
+GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT
 +
-!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

bio/kallisto/quant/test/reads/A_R2.fastq

@@ -1,4 +1,4 @@
 @1
-GCTAGC
+GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT
 +
-!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

bio/kallisto/quant/wrapper.py

@@ -20,10 +20,10 @@
 
 shell(
     "kallisto quant "  # Tool
-    "{extra} "  # Optional parameters
-    "--threads={snakemake.threads} "  # Number of threads
-    "--index={snakemake.input.index} "  # Input file
-    "--output-dir={snakemake.output} "  # Output directory
-    "{fastq} "  # Input FASTQ files
-    "{log}"  # Logging
+    " --threads {snakemake.threads}"  # Number of threads
+    " --index {snakemake.input.index}"  # Input file
+    " {extra}"  # Optional parameters
+    " --output-dir {snakemake.output}"  # Output directory
+    " {fastq}"  # Input FASTQ files
+    " {log}"  # Logging
 )