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Metagenomics
snakemake
Commits
0ddcffa4
Commit
0ddcffa4
authored
Nov 19, 2020
by
Kenzo-Hugo Hillion
♻
Browse files
add sams output to paired metaphlan
parent
d1e501f6
Changes
2
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tools/metaphlan3/metaphlan/paired/Snakefile
View file @
0ddcffa4
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@@ -24,6 +24,7 @@ rule metaphlan3_paired:
modules = __metaphlan3_modules,
input_type = __metaphlan3_input_type,
bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
sams = "{output_dir}/{sample}.sam.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
options = __metaphlan3_options
threads:
__metaphlan3_threads
...
...
@@ -31,5 +32,5 @@ rule metaphlan3_paired:
command = []
if params.modules:
command.append("module load {params.modules}")
command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} --bowtie2out {params.bowtie2out} {params.options} {input.r1},{input.r2} {output}")
command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type}
-s {params.sams}
--bowtie2out {params.bowtie2out} {params.options} {input.r1},{input.r2} {output}")
shell(" && ".join(command))
tools/metaphlan3/metaphlan/single/Snakefile
View file @
0ddcffa4
...
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@@ -15,7 +15,7 @@ rule metaphlan3:
modules = __metaphlan3_modules,
input_type = __metaphlan3_input_type,
bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
sams = "{output_dir}/{sample}.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
sams = "{output_dir}/{sample}.
sam.
bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}"),
options = __metaphlan3_options
threads:
__metaphlan3_threads
...
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