update metaphlan3 pipeline

tools/metaphlan3/metaphlan/paired/Snakefile

@@ -18,7 +18,7 @@ rule metaphlan3_paired:
         r1 = __metaphlan3_input_r1,
         r2 = __metaphlan3_input_r2
     output:
-        profile = __metaphlan3_output,
+        profile = __metaphlan3_output_profile,
         bowtie2out = __metaphlan3_output_bowtie2out,
         sams = __metaphlan3_output_sams
     params:

workflows/metaphlan3/README.md

+# Simple metaphlan3 workflows
+
+Workflows using metaphlan3 and simple visualization of the results.
+
+All examples presented were made for our TARS cluster system. This means you will be likely to find some
+absolute path into the `config.yaml` that you might not have access to.
+
+For every workflow, an example is provided and is based on the `config.yaml` file. Singularity images are necessary for these examples.

workflows/metaphlan3/paired_metaphlan2/Snakefile

+configfile: "config.yaml"
+
+# ==== Snakefile paths ====
+__metaphlan3_rules = config.get("snakefiles", {}).get("metaphlan3", "../../tools/metaphlan2/metaphlan2/Snakefile")
+__metaphlan2_merge_rules = config.get("snakefiles", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/Snakefile")
+__metaphlan2_heatmap_rules = config.get("snakefiles", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/Snakefile")
+__graphlan_from_metaphlan2_rules = config.get("snakefiles", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/Snakefile")
+
+__input_dir = config['input_dir']
+__main_output_dir = config.get('output_dir', 'output')
+
+# ---- Metaphlan3
+__metaphlan3_output_dir = __main_output_dir + "/metaphlan3"
+__metaphlan3_input_type = config['metaphlan3'].get('input_type', 'fastq')
+__metaphlan3_input_r1 = "{dir}/{sample}{ext}".format(dir=__input_dir,
+                                                      sample="{sample}",
+                                                      ext="_1.fq.gz")
+__metaphlan3_input_r2 = "{dir}/{sample}{ext}".format(dir=__input_dir,
+                                                      sample="{sample}",
+                                                      ext="_2.fq.gz")
+__metaphlan3_output_profile = "{dir}/{sample}.profile.tsv".format(dir=__metaphlan3_output_dir,
+                                                                  sample="{sample}")
+__metaphlan3_output_bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}")
+__metaphlan3_output_sams = "{output_dir}/{sample}.sam.bz2".format(output_dir=__metaphlan3_output_dir, sample="{sample}")
+
+include: __metaphlan3_rules
+
+# ---- Metaphlan2 merge
+__metaphlan2_merge_output_dir = __main_output_dir + "/metaphlan_merge"
+__metaphlan2_merge_output_file_name = config['metaphlan2_merge'].get('output_file_name',"merged_taxonomic_profiles.txt")
+__metaphlan2_merge_input = __metaphlan3_output_profile
+__metaphlan2_merge_output = "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
+                                                       file_name=__metaphlan2_merge_output_file_name)
+include: __metaphlan2_merge_rules
+
+# ---- Metaphlan2 heatmap
+__metaphlan2_heatmap_output_dir = __main_output_dir + "/metaphlan2_heatmap"
+__metaphlan2_heatmap_output_file_name = config['metaphlan2_heatmap'].get('output_name',"heatmap.png")
+__metaphlan2_heatmap_input = __metaphlan2_merge_output
+__metaphlan2_heatmap_output = "{dir}/{file_name}".format(dir=__metaphlan2_heatmap_output_dir,
+                                                         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.get("graphlan_from_metaphlan2", {}).get('output_name',"dendrogram.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:
+        heatmap = __metaphlan2_heatmap_output,
+        dendogram = __graphlan_from_metaphlan2_output
+

workflows/metaphlan3/paired_metaphlan2/config.yaml

+snakefiles:
+  metaphlan3: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/metaphlan3/metaphlan/paired/Snakefile
+  metaphlan2_merge: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
+  metaphlan2_heatmap: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/metaphlan2/metaphlan2_heatmap/Snakefile
+  graphlan_from_metaphlan2: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/subworkflows/graphlan_from_metaphlan2/Snakefile
+
+samples:
+  - sample_1
+  - sample_2
+  - sample_2
+
+input_dir: /a/path/to/input/data
+output_dir: metaphlan2_output
+
+metaphlan3:
+  modules: singularity
+  threads: 4
+  input_type: fastq
+  options: --bowtie2db /pasteur/gaia/projets/p01/Atm/DBs/bowtie2/metaphlan2/
+  exec_command: singularity exec --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/tools/metaphlan2/from_docker/metaphlan2_2.7.7_s3.2.1.simg metaphlan2.py
+
+metaphlan2_merge:
+  modules: singularity
+  exec_command: singularity exec --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/tools/metaphlan2/from_docker/metaphlan2_2.7.7_s3.2.1.simg merge_metaphlan_tables.py
+
+metaphlan2_heatmap:
+  modules: singularity
+  exec_command: singularity exec --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/tools/metaphlan2/from_docker/metaphlan2_2.6.0_s3.2.1.simg metaphlan_hclust_heatmap.py
+  output_name: snakemake_heatmap.png
+
+export2graphlan:
+  modules: singularity
+  exec_command: singularity exec --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/tools/graphlan/from_docker/graphlan_0.9.7_s3.2.1.simg export2graphlan.py
+  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:
+  modules: singularity
+  exec_command: singularity exec --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/tools/graphlan/from_docker/graphlan_0.9.7_s3.2.1.simg graphlan_annotate.py
+
+graphlan:
+  modules: singularity
+  exec_command: singularity exec --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/tools/graphlan/from_docker/graphlan_0.9.7_s3.2.1.simg graphlan.py
+  options: "--dpi 300 --external_legends"