diff --git a/workflows/simple_metaphlan2/SnakeFile b/workflows/simple_metaphlan2/SnakeFile index 4b5d7b244464387c64e92359b0156e3f0549d106..8f939955b32bcf28fbd533248bcc31fe72b3f717 100644 --- a/workflows/simple_metaphlan2/SnakeFile +++ b/workflows/simple_metaphlan2/SnakeFile @@ -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 diff --git a/workflows/simple_metaphlan2/config.yaml b/workflows/simple_metaphlan2/config.yaml index d2d4c9a10792af9d0ec3a8c81208c36423a79132..c8c0b9f99ca675a715e49aacbdc18dd8286bdfda 100644 --- a/workflows/simple_metaphlan2/config.yaml +++ b/workflows/simple_metaphlan2/config.yaml @@ -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" \ No newline at end of file