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perf: autobump bio/kallisto/index #1708

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Aug 1, 2023
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perf: autobump bio/kallisto/index #1708

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af48a97
perf: update bio/kallisto/index/environment.yaml.
snakedeploy-bot[bot] Jul 28, 2023
0450521
Added threads
fgvieira Aug 1, 2023
a54d380
Fix test file
fgvieira Aug 1, 2023
1a7ebc1
Update doc
fgvieira Aug 1, 2023
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2 changes: 1 addition & 1 deletion bio/kallisto/index/environment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ channels:
- bioconda
- nodefaults
dependencies:
- kallisto =0.48.0
- kallisto =0.50.0
7 changes: 7 additions & 0 deletions bio/kallisto/index/meta.yaml
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@@ -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
2 changes: 1 addition & 1 deletion bio/kallisto/index/test/transcriptome.fasta
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@@ -1,2 +1,2 @@
>Sheila
GCTAGCTCAGAAAAAAAAAA
GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT
11 changes: 6 additions & 5 deletions bio/kallisto/index/wrapper.py
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Expand Up @@ -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
)
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