PICARD COLLECTRNASEQMETRICS¶
Run picard CollectRnaSeqMetrics to generate QC metrics for RNA-seq data.
URL:
Example¶
This wrapper can be used in the following way:
rule alignment_summary:
input:
# BAM aligned, splicing-aware, to reference genome
bam="mapped/a.bam",
# Annotation file containing transcript, gene, and exon data
refflat="annotation.refFlat"
output:
"results/a.rnaseq_metrics.txt"
params:
# strand is optional (defaults to NONE) and pertains to the library preparation
# options are FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND, and NONE
strand="NONE",
# optional additional parameters, for example,
extra="VALIDATION_STRINGENCY=STRICT"
log:
"logs/picard/rnaseq-metrics/a.log"
# optional specification of memory usage of the JVM that snakemake will respect with global
# resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
# and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
# https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
resources:
mem_mb=1024
wrapper:
"https://raw.githubusercontent.com/brcopeland/snakemake-wrappers/picard_collectrnaseqmetrics/bio/picard/collectrnaseqmetrics"
#"0.85.0/bio/picard/collectrnaseqmetrics"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Software dependencies¶
picard==2.25.4
snakemake-wrapper-utils==0.1.3
Input/Output¶
Input:
- BAM file of RNA-seq data aligned to genome
- REF_FLAT formatted file of transcriptome annotations
Output:
- RNA-Seq metrics text file
Notes¶
- For more information, see https://broadinstitute.github.io/picard/command-line-overview.html#CollectRnaSeqMetrics.
Authors¶
- Brett Copeland
Code¶
__author__ = "Brett Copeland"
__copyright__ = "Copyright 2021, Brett Copeland"
__email__ = "brcopeland@ucsd.edu"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
strand = snakemake.params.get("strand", "NONE")
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"picard CollectRnaSeqMetrics "
"{java_opts} {extra} "
"INPUT={snakemake.input.bam} "
"OUTPUT={snakemake.output} "
"REF_FLAT={snakemake.input.refflat} "
"STRAND_SPECIFICITY={strand} "
"{log}"
)