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>

bio/cutadapt/pe/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - cutadapt ==3.4
+  - cutadapt =4.1

bio/cutadapt/pe/meta.yaml

@@ -1,6 +1,7 @@
 name: cutadapt-pe
 description: |
   Trim paired-end reads using cutadapt.
+url: https://github.com/marcelm/cutadapt
 authors:
   - Julian de Ruiter
   - David Laehnemann
@@ -9,3 +10,6 @@ input:
 output:
   - two trimmed (paired-end) fastq files
   - text file containing trimming statistics
+notes: |
+  * The `extra` param allows for additional program arguments.
+  * The `adapters` param allows for separatelly specifying adapter options (optional).

bio/cutadapt/pe/test/Snakefile

@@ -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"

bio/cutadapt/pe/wrapper.py

@@ -22,11 +22,11 @@
 
 shell(
     "cutadapt"
+    " --cores {snakemake.threads}"
     " {adapters}"
     " {extra}"
     " -o {snakemake.output.fastq1}"
     " -p {snakemake.output.fastq2}"
-    " -j {snakemake.threads}"
     " {snakemake.input}"
     " > {snakemake.output.qc} {log}"
 )

bio/cutadapt/se/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - cutadapt ==3.4
+  - cutadapt =4.1

bio/cutadapt/se/meta.yaml

@@ -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).

bio/cutadapt/se/test/Snakefile

@@ -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"

bio/cutadapt/se/wrapper.py

@@ -22,9 +22,9 @@
 
 shell(
     "cutadapt"
+    " --cores {snakemake.threads}"
     " {adapters}"
     " {extra}"
-    " -j {snakemake.threads}"
     " -o {snakemake.output.fastq}"
     " {snakemake.input[0]}"
     " > {snakemake.output.qc} {log}"