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Metagenomics
snakemake
Commits
8c192e82
Commit
8c192e82
authored
May 13, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
add subworkflow part and subworkflow metaphlan to graphlan
parent
2462bf79
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2
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workflows/subworfklows/README.md
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8c192e82
# 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.
workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
0 → 100644
View file @
8c192e82
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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