Commit 8bb596da authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add graphlan to metaphlan2 workflow

parent 8c192e82
......@@ -4,6 +4,7 @@ configfile: "config.yaml"
__metaphlan2_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
__metaphlan2_merge_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
__metaphlan2_heatmap_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
__graphlan_from_metaphlan2_rules = "../subworkflows/graphlan_from_metaphlan2/SnakeFile"
__input_dir = config['input_dir']
__main_output_dir = config.get('output_dir', 'output')
......@@ -36,6 +37,15 @@ __metaphlan2_heatmap_output = "{dir}/{file_name}".format(dir=__metaphlan2_heatma
file_name=__metaphlan2_heatmap_output_file_name)
include: __metaphlan2_heatmap_rules
# ---- Graphlan Dendogram
__graphlan_from_metaphlan2_output_dir = __main_output_dir + "/graphlan"
__graphlan_from_metaphlan2_output_file_name = config['graphlan_from_metaphlan2'].get('output_name',"dendogram.png")
__graphlan_from_metaphlan2_input = __metaphlan2_merge_output
__graphlan_from_metaphlan2_output = "{dir}/{file_name}".format(dir=__graphlan_from_metaphlan2_output_dir,
file_name=__graphlan_from_metaphlan2_output_file_name)
include: __graphlan_from_metaphlan2_rules
rule all:
input:
__metaphlan2_heatmap_output
heatmap: __metaphlan2_heatmap_output,
dendogram: __graphlan_from_metaphlan2_output
......@@ -20,3 +20,14 @@ metaphlan2_merge:
metaphlan2_heatmap:
exec_command: singularity run --app heatmap --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/metaphlan2/metaphlan2.simg
output_name: snakemake_heatmap.png
export2graphlan:
exec_command: singularity run --app export2graphlan --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/graphlan/graphlan.simg
options: "--skip_rows 1,2 --most_abundant 100 --abundance_threshold 1 --least_biomarkers 10 --annotations 5,6 --external_annotations 7 --min_clade_size 1"
graphlan_annotate:
exec_command: singularity run --app graphlan_annotate --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/graphlan/graphlan.simg
graphlan:
exec_command: singularity run --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/graphlan/graphlan.simg
options: "--dpi 300 --external_legends"
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