Commit 83f0eae8 authored by Valentina Galata's avatar Valentina Galata
Browse files

rna filtering: bbmap/bbduk: mv filt params to config; minor change in output...

rna filtering: bbmap/bbduk: mv filt params to config; minor change in output streams (issue #12) [ci skip]
parent 99ce25b0
Pipeline #42581 skipped
......@@ -41,6 +41,8 @@ filtering:
filter: hg38
rnafiltering:
tool: "sortmerna" # sortmerna (default), bbduk (from bbmap tools)
bbduk: # bbduk-specific parameters (used only if bbduk is enabled)
filt: "k=27 qhdist=1 mkh=1" # filtering params; see https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/
files:
- rfam-5.8s-database-id98
- silva-arc-16s-id95
......
......@@ -123,6 +123,12 @@ properties:
- "sortmerna"
- "bbduk"
default: "sortmerna"
bbduk:
type: object
properties:
filt:
type: string
default: "k=27 qhdist=1 mkh=1"
assembly:
type: object
properties:
......
......@@ -77,8 +77,8 @@ elif config["rnafiltering"]["tool"] == "bbduk":
mem = MEMCORE,
# from manual: ca. 85% of the machine’s physical memory
mem2="-Xmx%dg" % round(8 * int(MEMCORE[:-1]) * 0.85),
# filtering (trade-off between sens and spec, affects memory/runtime)
filt="k=27 qhdist=1 mkh=1", # (issue #12)
# filtering params
filt=config["rnafiltering"]["bbduk"]["filt"],
# incl. rev. complement, quality = auto, do not zip, keep read order
misc="rcomp=t qin=auto qout=auto ziplevel=1 ordered=t"
conda:
......@@ -91,7 +91,7 @@ elif config["rnafiltering"]["tool"] == "bbduk":
"""
(
refs=$(echo \"{input.refs}\" | tr ' ' ',') &&
bbduk.sh in={input.r1} in2={input.r2} out={output.r1u} out2={output.r2u} outm={output.r1m} outm2={output.r2m} ref=${{refs}} refstats={output.stats_pe} threads={threads} {params.mem2} {params.filt} {params.misc} &&
bbduk.sh in1={input.r1} in2={input.r2} out1={output.r1u} out2={output.r2u} outm1={output.r1m} outm2={output.r2m} ref=${{refs}} refstats={output.stats_pe} threads={threads} {params.mem2} {params.filt} {params.misc} &&
bbduk.sh in={input.se} out={output.seu} outm={output.sem} ref=${{refs}} refstats={output.stats_se} threads={threads} {params.mem2} {params.filt} {params.misc}
) &> {log}
"""
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