Merge branch '21-metaphlan3' into 'master'

update metaphlan3 and add strainphlan

Closes #22

See merge request !6

tools/eggnogmapper2/annotate/example_usage/config.yaml

 snakefiles:
-    eggnogmapper2_annotate: /pasteur/projets/policy01/Atm/snakemake/tools/eggnogmapper2/annotate/Snakefile
+    eggnogmapper2_annotate: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/eggnogmapper2/annotate/Snakefile
 
 input_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output/eggnogmapper2/diamond/
 output_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output

tools/eggnogmapper2/diamond/example_usage/config.yaml

 snakefiles:
-    eggnogmapper2_diamond: /pasteur/projets/policy01/Atm/snakemake/tools/eggnogmapper2/diamond/Snakefile
+    eggnogmapper2_diamond: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/eggnogmapper2/diamond/Snakefile
 
 input_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output/split_fasta
 output_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output

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:

tools/strainphlan/extract_markers/README.md

+# extract_markers.py for strainphlan
+
+This step will extract the markers of selected species from MetaPhlAn database.
+
+### Help section
+
+```
+usage: extract_markers.py [-h] [-d DATABASE] [-c CLADE] [-o OUTPUT_DIR]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -d DATABASE, --database DATABASE
+                        The input MetaPhlAn dtabase
+  -c CLADE, --clade CLADE
+                        The clades to investigate
+  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
+                        The output directory
+```

tools/strainphlan/sample2markers/README.md

@@ -2,6 +2,9 @@
 
 This step will reconstruct all species strains found in metaphlan output sam file and store them in a pickle file (*.pkl). Those strains are referred as sample-reconstructed strains.
 
+.. **Note**: output pkl file is written should be written in a individual directory since the script tries
+    to create and write into a `tmp` dir that leads to error when running sample2markers.py in parallel.
+
 ### Help section
 
 ```

tools/strainphlan/strainphlan/README.md

+# extract_markers.py for strainphlan
+
+This step will build the multiple sequence alignment and the phylogenetic tree for each species.
+
+### Help section
+
+```
+usage: strainphlan [-h] [-d DATABASE] [-m CLADE_MARKERS]
+                   [-s SAMPLES [SAMPLES ...]] [-r REFERENCES [REFERENCES ...]]
+                   [-c CLADE] [-o OUTPUT_DIR] [-n NPROCS]
+                   [--secondary_samples SECONDARY_SAMPLES [SECONDARY_SAMPLES ...]]
+                   [--secondary_references SECONDARY_REFERENCES [SECONDARY_REFERENCES ...]]
+                   [--trim_sequences TRIM_SEQUENCES]
+                   [--marker_in_n_samples MARKER_IN_N_SAMPLES]
+                   [--sample_with_n_markers SAMPLE_WITH_N_MARKERS]
+                   [--secondary_sample_with_n_markers SECONDARY_SAMPLE_WITH_N_MARKERS]
+                   [--phylophlan_mode {accurate,fast}]
+                   [--phylophlan_configuration PHYLOPHLAN_CONFIGURATION]
+                   [--mutation_rates] [--print_clades_only]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -d DATABASE, --database DATABASE
+                        The input MetaPhlAn 3.0 database (default: /pasteur/so
+                        nic/homes/kehillio/miniconda3/envs/mpa/lib/python3.7/s
+                        ite-packages/metaphlan/metaphlan_databases/mpa_v30_CHO
+                        COPhlAn_201901.pkl)
+  -m CLADE_MARKERS, --clade_markers CLADE_MARKERS
+                        The clade markers as FASTA file (default: None)
+  -s SAMPLES [SAMPLES ...], --samples SAMPLES [SAMPLES ...]
+                        The reconstructed markers for each sample (default:
+                        [])
+  -r REFERENCES [REFERENCES ...], --references REFERENCES [REFERENCES ...]
+                        The reference genomes (default: [])
+  -c CLADE, --clade CLADE
+                        The clade to investigate (default: None)
+  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
+                        The output directory (default: None)
+  -n NPROCS, --nprocs NPROCS
+                        The number of threads to use (default: 1)
+  --secondary_samples SECONDARY_SAMPLES [SECONDARY_SAMPLES ...]
+                        The reconstructed markers for each secondary sample
+                        (default: [])
+  --secondary_references SECONDARY_REFERENCES [SECONDARY_REFERENCES ...]
+                        The secondary reference genomes (default: [])
+  --trim_sequences TRIM_SEQUENCES
+                        The number of bases to remove from both ends when
+                        trimming markers (default: 50)
+  --marker_in_n_samples MARKER_IN_N_SAMPLES
+                        Theshold defining the minimum percentage of samples to
+                        keep a marker (default: 80)
+  --sample_with_n_markers SAMPLE_WITH_N_MARKERS
+                        Threshold defining the minimun number of markers to
+                        keep a sample (default: 20)
+  --secondary_sample_with_n_markers SECONDARY_SAMPLE_WITH_N_MARKERS
+                        Threshold defining the minimun number of markers to
+                        keep a secondary sample (default: 20)
+  --phylophlan_mode {accurate,fast}
+                        The presets for fast or accurate phylogenetic analysis
+                        (default: accurate)
+  --phylophlan_configuration PHYLOPHLAN_CONFIGURATION
+                        The PhyloPhlAn configuration file (default: None)
+  --mutation_rates      If specified will produced a mutation rates table for
+                        each of the aligned markers and a summary table for
+                        the concatenated MSA. This operation can take long
+                        time to finish (default: False)
+  --print_clades_only   If specified only print the potential clades and stop
+                        without building any tree (default: False)
+```

tools/strainphlan/strainphlan/Snakefile

+__strainphlan_exec_command = config.get('strainphlan', {}).get('exec_command', 'strainphlan')
+__strainphlan_modules = config.get('strainphlan', {}).get('modules')
+__strainphlan_options = config.get('strainphlan', {}).get('options', "")
+__strainphlan_threads = config.get('strainphlan', {}).get('threads', 1)
+
+
+rule strainphlan:
+    input:
+        __strainphlan_input
+    output:
+        __strainphlan_output
+    params:
+        exec_command = __strainphlan_exec_command,
+        modules = __strainphlan_modules,
+        clade = __strainphlan_clade,
+        output_dir = __strainphlan_output_dir,
+        options = __strainphlan_options
+    threads:
+        __strainphlan_threads
+    run:
+        command = []
+        if params.modules:
+            command.append("module load {params.modules}")
+        command.append("{params.exec_command} -s {input} -n {threads} -c {params.clade} {params.options} -o {params.output_dir}")
+        shell(" && ".join(command))

tools/strainphlan/strainphlan/config.yaml

+input_dir: data
+
+strainphlan:
+  threads: 4
+  exec_command: sample2markers.py

tools/utils/cat/example_usage/config.yaml

 snakefiles:
-    cat: /pasteur/projets/policy01/Atm/snakemake/tools/utils/cat/Snakefile
+    cat: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/utils/cat/Snakefile
 
 input_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output/eggnogmapper2/diamond/
 output_dir: /pasteur/projets/policy01/Atm/kenzo/sandbox/20200210_test_snakemake/test_output

tools/utils/split_fasta/example_usage/config.yaml

 snakefiles:
-    split_fasta: /pasteur/projets/policy01/Atm/snakemake/tools/utils/split_fasta/Snakefile
+    split_fasta: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/utils/split_fasta/Snakefile
 
 input_fasta: /pasteur/projets/policy01/DBs/IGC/2014-9.9M/IGC.fa
 output_dir: /pasteur/projets/policy01/sandbox/20200210_test_snakemake/output

workflows/eggnogmapperv2/config.yaml

 snakefiles:
-    eggnogmapper2_diamond: /pasteur/projets/policy01/Atm/snakemake/tools/eggnogmapper2/diamond/Snakefile
-    split_fasta: /pasteur/projets/policy01/Atm/snakemake/tools/utils/split_fasta/Snakefile
-    cat: /pasteur/projets/policy01/Atm/snakemake/tools/utils/cat/Snakefile
-    eggnogmapper2_annotate: /pasteur/projets/policy01/Atm/snakemake/tools/eggnogmapper2/annotate/Snakefile
+    eggnogmapper2_diamond: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/eggnogmapper2/diamond/Snakefile
+    split_fasta: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/utils/split_fasta/Snakefile
+    cat: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/utils/cat/Snakefile
+    eggnogmapper2_annotate: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/eggnogmapper2/annotate/Snakefile
 
 input_fasta: /pasteur/homes/kehillio/Atm/kenzo/sandbox/20200210_test_snakemake/test.fa
 output_dir: /pasteur/homes/kehillio/Atm/kenzo/sandbox/20200210_test_snakemake/test_output

workflows/metaphlan2/paired_metaphlan2/config.yaml

 snakefiles:
-  metaphlan2: /pasteur/projets/policy01/Atm/snakemake/tools/metaphlan2/metaphlan2/paired/Snakefile
-  metaphlan2_merge: /pasteur/projets/policy01/Atm/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
-  metaphlan2_heatmap: /pasteur/projets/policy01/Atm/snakemake/tools/metaphlan2/metaphlan2_heatmap/Snakefile
-  graphlan_from_metaphlan2: /pasteur/projets/policy01/Atm/snakemake/subworkflows/graphlan_from_metaphlan2/Snakefile
+  metaphlan2: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/metaphlan2/metaphlan2/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

workflows/metaphlan2/single_metaphlan2/config.yaml

 snakefiles:
-  metaphlan2: /pasteur/projets/policy01/Atm/snakemake/tools/metaphlan2/metaphlan2/single/Snakefile
-  metaphlan2_merge: /pasteur/projets/policy01/Atm/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
-  metaphlan2_heatmap: /pasteur/projets/policy01/Atm/snakemake/tools/metaphlan2/metaphlan2_heatmap/Snakefile
-  graphlan_from_metaphlan2: /pasteur/projets/policy01/Atm/snakemake/subworkflows/graphlan_from_metaphlan2/Snakefile
+  metaphlan2: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/metaphlan2/metaphlan2/single/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

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"

workflows/strainphlan/README.md

+# StrainPhlan
+
+This describes a workflow to run [strainphlan](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0)
+
+In brief it contains 4 steps:
+
+* Run Metaphlan on all samples (paired-ends)
+* Extract markers from metaphlan outputs
+* Run StrainPhlan on all selected clades
\ No newline at end of file

workflows/strainphlan/Snakefile

+configfile: "config.yaml"
+
+# ==== Snakefile paths ====
+__metaphlan3_rules = config.get("snakefiles", {}).get("metaphlan3")
+__metaphlan2_merge_rules = config.get("snakefiles", {}).get("metaphlan2_merge")
+__sample2markers_rules = config.get("snakefiles", {}).get("sample2markers")
+__strainphlan_rules = config.get("snakefiles", {}).get("strainphlan")
+
+__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 = expand("{dir}/{sample}.profile.tsv".format(dir=__metaphlan3_output_dir,
+                                                                      sample="{sample}"),
+                                  sample=config['samples'])
+__metaphlan2_merge_output = "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
+                                                       file_name=__metaphlan2_merge_output_file_name)
+include: __metaphlan2_merge_rules
+
+rule metaphlan_merge_all:
+    input:
+        "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
+                                   file_name=__metaphlan2_merge_output_file_name)
+
+# ---- Sample2markers ----
+__sample2markers_main_output_dir = __main_output_dir + "/sample2markers"
+__sample2markers_output_dir = "{dir}/{sample}".format(dir=__sample2markers_main_output_dir,
+                                                      sample="{sample}")
+__sample2markers_input = __metaphlan3_output_sams
+__sample2markers_output = "{dir}/{sample}.pkl".format(dir=__sample2markers_output_dir,
+                                                      sample="{sample}")
+
+include: __sample2markers_rules
+
+
+# ---- StrainPhlan ----
+
+__strainphlan_main_output_dir = __main_output_dir + "/strainphlan"
+__strainphlan_clade = "{clade}"
+__strainphlan_output_dir = "{dir}/{clade}".format(dir=__strainphlan_main_output_dir,
+                                                  clade="{clade}")
+
+__strainphlan_input = expand("{dir}/{sample}.pkl".format(dir=__sample2markers_output_dir,
+                                                    sample="{sample}"),
+                             sample=config['samples'])
+__strainphlan_output = "{dir}/{prefix}.{clade}.{ext}".format(dir=__strainphlan_output_dir,
+                                                             prefix="RAxML_bestTree",
+                                                             clade="{clade}",
+                                                             ext="StrainPhlAn3.tre")
+
+include: __strainphlan_rules
+
+
+rule all:
+    input:
+        expand("{dir}/{prefix}.{clade}.{ext}".format(dir=__strainphlan_output_dir,
+                                                             prefix="RAxML_bestTree",
+                                                             clade="{clade}",
+                                                             ext="StrainPhlAn3.tre"),
+               clade=config['strainphlan']['clades'])

workflows/strainphlan/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
+  sample2markers: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/strainphlan/sample2markers/Snakefile
+  strainphlan: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/strainphlan/strainphlan/Snakefile
+
+samples:
+  - sample_1
+  - sample_2
+  - sample_2
+
+input_dir: /a/path/to/input/data
+output_dir: output
+
+metaphlan3:
+  threads: 4
+  input_type: fastq
+  options: --bowtie2db /pasteur/zeus/projets/p02/metasig/DBs/metaphlan/metaphlan3bowtie2db/ --index mpa_v30_CHOCOPhlAn_201901
+
+metaphlan2_merge:
+  threads: 1
+
+sample2markers:
+  threads: 4
+
+strainphlan:
+  threads: 8
+  options: ""
+  clades:
+    - s__Escherichia_coli
+    - s__Klebsiella_pneumoniae