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79 changes: 79 additions & 0 deletions bio/trimmomatic/environment.linux-64.pin.txt
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# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
# created-by: conda 25.5.0
@EXPLICIT
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7 changes: 7 additions & 0 deletions bio/trimmomatic/environment.yaml
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channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- trimmomatic =0.39
- snakemake-wrapper-utils =0.7.2
20 changes: 20 additions & 0 deletions bio/trimmomatic/meta.yaml
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name: "trimmomatic pe"
description: Trim reads with Trimmomatic.
url: http://www.usadellab.org/cms/?page=trimmomatic
authors:
- Johannes Köster
- Jorge Langa
- Filipe G. Vieira
input:
- r1: fastq(gz) file
- r2: fastq(gz) file (if PE)
output:
- r1: trimmed R1 fastq(gz) file
- r2: trimmed R2 fastq(gz) file (if PE)
- r1_unpaired: unpaired R1 fastq(gz) file (if PE)
- r2_unpaired: unpaired R2 fastq(gz) file (if PE)
params:
- trimmer: trimming steps
- extra: additional program arguments
notes: |
For PE (paired-end) trimming, all output files need to be specified.
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27 changes: 0 additions & 27 deletions bio/trimmomatic/pe/test/Snakefile_gz_fq

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28 changes: 0 additions & 28 deletions bio/trimmomatic/pe/test/Snakefile_gz_gz

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104 changes: 0 additions & 104 deletions bio/trimmomatic/pe/wrapper.py

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8 changes: 0 additions & 8 deletions bio/trimmomatic/se/environment.yaml

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1 change: 0 additions & 1 deletion bio/trimmomatic/se/test/Snakefile

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22 changes: 0 additions & 22 deletions bio/trimmomatic/se/test/Snakefile_fq_fq

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