Commit 8c192e82 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add subworkflow part and subworkflow metaphlan to graphlan

parent 2462bf79
# Snakemake subworkflows
Similar to tools, subworkflows cannot be used directly but need to be called in a higher Snakefile
by setting up the required variables.
configfile: "config.yaml"
"""
This subworkflow need to be called to be used by specifying:
- __graphlan_from_metaphlan2_input
- __graphlan_from_metaphlan2_output
- __graphlan_from_metaphlan2_output_dir
"""
# ==== Rule paths ====
__export2graphlan_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
__graphlan_annotate_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
__graphlan_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
# ---- export2graphlan
__export2graphlan_input = __graphlan_from_metaphlan2_input
__export2graphlan_output_tree = __graphlan_from_metaphlan2_output + ".tree.txt"
__export2graphlan_output_annotation = __graphlan_from_metaphlan2_output + ".annot.txt"
include: __export2graphlan_rules
# ---- graphlan_annotate
__graphlan_annotate_input_tree = __export2graphlan_output_tree
__graphlan_annotate_input_annotation = __export2graphlan_output_annotation
__graphlan_annotate_output = __graphlan_from_metaphlan2_output + ".annot.xml"
include: __graphlan_annotate_rules
# ---- graphlan
__graphlan_input = __graphlan_annotate_output
__graphlan_output = __graphlan_from_metaphlan2_output
include: __graphlan_rules
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