Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Menu
Open sidebar
Midoux Cedric
workflow_metagenomics
Commits
7d94c2f8
Commit
7d94c2f8
authored
Sep 05, 2019
by
Midoux Cedric
Browse files
contigs_input(wildcards)
parent
4dcb27bf
Changes
2
Hide whitespace changes
Inline
Side-by-side
assembly.smk
View file @
7d94c2f8
...
...
@@ -93,3 +93,9 @@ rule metaspades:
"-i work/metaSPADES/{wildcards.reads}/contigs.fasta "
"-o {output.contigs} "
"--min-length {params.min_len} "
def contigs_input(wildcards):
if config["ASSEMBLER"] == "megahit":
return ["work/megahit/{wildcards.sample}/{wildcards.sample}.contigs.fa".format(wildcards=wildcards)]
elif config["ASSEMBLER"] == "metaspades":
return ["work/metaSPADES/{wildcards.sample}/{wildcards.sample}.contigs.fasta".format(wildcards=wildcards)]
global.smk
View file @
7d94c2f8
...
...
@@ -8,6 +8,7 @@ rule all:
input:
"report/multiqc_report.html",
expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
"report/contigs_coassembly-taxNames.tsv",
include: "../workflow_metagenomics/quality.smk"
include: "../workflow_metagenomics/preprocess.smk"
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment