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perf: updated cutadapt version, formatted files, and improved docs. (#…
…505) * Updated cutadapt version, formated files, and improved docs. * Small version fix * Change channel order due to new strict policy Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
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@@ -3,4 +3,4 @@ channels: | |
- bioconda | ||
- nodefaults | ||
dependencies: | ||
- cutadapt ==3.4 | ||
- cutadapt =4.1 |
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@@ -1,17 +1,17 @@ | ||
rule cutadapt: | ||
input: | ||
["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"] | ||
["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], | ||
output: | ||
fastq1="trimmed/{sample}.1.fastq", | ||
fastq2="trimmed/{sample}.2.fastq", | ||
qc="trimmed/{sample}.qc.txt" | ||
qc="trimmed/{sample}.qc.txt", | ||
params: | ||
# https://cutadapt.readthedocs.io/en/stable/guide.html#adapter-types | ||
adapters="-a AGAGCACACGTCTGAACTCCAGTCAC -g AGATCGGAAGAGCACACGT -A AGAGCACACGTCTGAACTCCAGTCAC -G AGATCGGAAGAGCACACGT", | ||
# https://cutadapt.readthedocs.io/en/stable/guide.html# | ||
extra="--minimum-length 1 -q 20" | ||
extra="--minimum-length 1 -q 20", | ||
log: | ||
"logs/cutadapt/{sample}.log" | ||
threads: 4 # set desired number of threads here | ||
"logs/cutadapt/{sample}.log", | ||
threads: 4 # set desired number of threads here | ||
wrapper: | ||
"master/bio/cutadapt/pe" |
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -3,4 +3,4 @@ channels: | |
- bioconda | ||
- nodefaults | ||
dependencies: | ||
- cutadapt ==3.4 | ||
- cutadapt =4.1 |
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@@ -1,10 +1,14 @@ | ||
name: cutadapt-se | ||
description: | | ||
Trim single-end reads using cutadapt. | ||
url: https://github.com/marcelm/cutadapt | ||
authors: | ||
- Julian de Ruiter | ||
input: | ||
- fastq file | ||
output: | ||
- trimmed fastq file | ||
- text file containing trimming statistics | ||
notes: | | ||
* The `extra` param allows for additional program arguments. | ||
* The `adapters` param allows for separatelly specifying adapter options (optional). |
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@@ -1,14 +1,14 @@ | ||
rule cutadapt: | ||
input: | ||
"reads/{sample}.fastq" | ||
"reads/{sample}.fastq", | ||
output: | ||
fastq="trimmed/{sample}.fastq", | ||
qc="trimmed/{sample}.qc.txt" | ||
qc="trimmed/{sample}.qc.txt", | ||
params: | ||
adapters="-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", | ||
extra="-q 20" | ||
extra="-q 20", | ||
log: | ||
"logs/cutadapt/{sample}.log" | ||
threads: 4 # set desired number of threads here | ||
"logs/cutadapt/{sample}.log", | ||
threads: 4 # set desired number of threads here | ||
wrapper: | ||
"master/bio/cutadapt/se" |
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