| trimmomatic |
2 |
- data/trimmed/trimmed.file1.fastq.gz
- data/trimmed/trimmed.file2.fastq.gz
|
|
- trimmomatic ==0.36
- pigz ==2.3.4
|
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75 | """
bio/trimmomatic/se
Snakemake wrapper to trim reads with trimmomatic in SE mode with help of pigz.
pigz is the parallel implementation of gz. Trimmomatic spends most of the time
compressing and decompressing instead of trimming sequences. By using process
substitution (<(command), >(command)), we can accelerate trimmomatic a lot.
Consider providing this wrapper with at least 1 extra thread per each gzipped
input or output file.
"""
__author__ = "Johannes Köster, Jorge Langa"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
# Distribute available threads between trimmomatic itself and any potential pigz instances
def distribute_threads(input_file, output_file, available_threads):
gzipped_input_files = 1 if input_file.endswith(".gz") else 0
gzipped_output_files = 1 if output_file.endswith(".gz") else 0
potential_threads_per_process = available_threads // (1 + gzipped_input_files + gzipped_output_files)
if potential_threads_per_process > 0:
# decompressing pigz creates at most 4 threads
pigz_input_threads = min(4, potential_threads_per_process) if gzipped_input_files != 0 else 0
pigz_output_threads = \
(available_threads - pigz_input_threads * gzipped_input_files) // (1 + gzipped_output_files) \
if gzipped_output_files != 0 else 0
trimmomatic_threads = available_threads - pigz_input_threads * gzipped_input_files - \
pigz_output_threads * gzipped_output_files
else:
# not enough threads for pigz
pigz_input_threads = 0
pigz_output_threads = 0
trimmomatic_threads = available_threads
return trimmomatic_threads, pigz_input_threads, pigz_output_threads
def compose_input_gz(filename, threads):
if filename.endswith(".gz") and threads > 0:
return "<(pigz -p {threads} --decompress --stdout {filename})".format(
threads=threads,
filename=filename
)
return filename
def compose_output_gz(filename, threads, compression_level):
if filename.endswith(".gz") and threads > 0:
return ">(pigz -p {threads} {compression_level} > {filename})".format(
threads=threads,
compression_level=compression_level,
filename=filename
)
return filename
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
compression_level = snakemake.params.get("compression_level", "-5")
trimmer = " ".join(snakemake.params.trimmer)
# Distribute threads
trimmomatic_threads, input_threads, output_threads = distribute_threads(
snakemake.input[0], snakemake.output[0], snakemake.threads
)
# Collect files
input = compose_input_gz(snakemake.input[0], input_threads)
output = compose_output_gz(snakemake.output[0], output_threads, compression_level)
shell("trimmomatic SE -threads {trimmomatic_threads} {extra} {input} {output} {trimmer} {log}")
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