diff --git a/tools/README.md b/tools/README.md
index c1df281bdf8e9bc9159fca5c6384a1fd6195efbd..0dc761d94c1cdd56f7d5cea458053534dfafaadd 100644
--- a/tools/README.md
+++ b/tools/README.md
@@ -7,14 +7,14 @@ This directory contains all tool descriptions that can be imported and used with
All tools are described in a `Snakefile` in a directory having its name.
All Snakefiles try to respect some rules and best practices in their design:
-* Reference to options from a `config.yaml` file
+* Reference to options from a `config_example.yaml` file
* Tool description
### Reference to options from `config.yaml` file
First part correspond to all options that are set up from a `config.yaml` file. They all have the nomenclature `__TOOLNAME_variable`.
-Then in the YAML `config.yaml` file, you can set the variable as followed:
+Then in the YAML `config_example.yaml` file, you can set the variable as followed:
```yaml
TOOLNAME:
@@ -31,17 +31,18 @@ config['TOOLNAME'].get('variable', 1)
In order to ease the linking of tools in a workflow, every parts of the tool is described as followed:
- * input with the nomenclature: `__TOOLNAME_input`
- * output with the nomenclature: ` __TOOLNAME_output`
- * params with different options that are described above
- * There is usually a `exec_command` to give the possibility to change the way the tool is called (locally installed, singularity ...)
- * There is usually a `options` to specify all other command line options. _You can still give a more detailed level of description for the options_
- * the shell command
+* input with the nomenclature: `__TOOLNAME_input`
+* output with the nomenclature: ` __TOOLNAME_output`
+* params with different options that are described above
+ * There is usually a `exec_command` to give the possibility to change the way the tool is called (locally installed, singularity ...)
+ * There is usually a `options` to specify all other command line options. _You can still give a more detailed level of description for the options_
+* the shell command
input and output are then set up in the workflow `Snakefile` that refer to the rule.
Therefore the rules cannot be used directly.
+> **Info**: You have noticed the possibility to give `modules` this is dedicated to our HPC that have some tools accessible via `module`.
+
## Example
-The directory for metaphlan2 rules give some example on the way to call the rules as well as setting
-the parameters in the `config.yaml` file.
+To find out example, refer to the workflow based on this tool descriptions in the `/workflows/` section.
diff --git a/tools/metaphlan2/metaphlan2/paired/Snakefile b/tools/metaphlan2/metaphlan2/paired/Snakefile
new file mode 100644
index 0000000000000000000000000000000000000000..0a06bd9882efaa9dcb2bac60fabb84e6b8b78db0
--- /dev/null
+++ b/tools/metaphlan2/metaphlan2/paired/Snakefile
@@ -0,0 +1,35 @@
+__metaphlan2_exec_command = config.get('metaphlan2', {}).get('exec_command', 'metaphlan2.py')
+__metaphlan2_modules = config.get('metaphlan2', {}).get('modules')
+__metaphlan2_input_type = config['metaphlan2'].get('input_type', 'fastq')
+__metaphlan2_options = config.get('metaphlan2', {}).get('options', "")
+__metaphlan2_threads = config.get('metaphlan2', {}).get('threads', 1)
+
+
+rule metaphlan2_paired:
+ """
+ MetaPhlAn 2 can also natively handle paired-end metagenomes (but does not use the paired-end information),
+ and, more generally, metagenomes stored in multiple files (but you need to specify the --bowtie2out parameter):
+
+ $ metaphlan2.py metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5
+ --input_type fastq > profiled_metagenome.txt
+
+ """
+ input:
+ r1 = __metaphlan2_input_r1,
+ r2 = __metaphlan2_input_r2
+ output:
+ __metaphlan2_output
+ params:
+ exec_command = __metaphlan2_exec_command,
+ modules = __metaphlan2_modules,
+ input_type = __metaphlan2_input_type,
+ bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan2_output_dir, sample="{sample}"),
+ options = __metaphlan2_options
+ threads:
+ __metaphlan2_threads
+ run:
+ command = []
+ if params.modules:
+ command.append("module load {params.modules}")
+ command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} --bowtie2out {params.bowtie2out} {params.options} {input.r1},{input.r2} {output}")
+ shell(" && ".join(command))
diff --git a/tools/metaphlan2/metaphlan2/paired/config_example.yaml b/tools/metaphlan2/metaphlan2/paired/config_example.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..a66651100333ccdd6760b1002dcf3c5fca75ede0
--- /dev/null
+++ b/tools/metaphlan2/metaphlan2/paired/config_example.yaml
@@ -0,0 +1,8 @@
+input_dir: data
+
+metaphlan2:
+ threads: 1
+ input_type: fastq
+ options: ""
+ pair_suffix: ""
+ exec_command: metaphlan2.py
diff --git a/tools/metaphlan2/metaphlan2/Snakefile b/tools/metaphlan2/metaphlan2/single/Snakefile
similarity index 73%
rename from tools/metaphlan2/metaphlan2/Snakefile
rename to tools/metaphlan2/metaphlan2/single/Snakefile
index 4203f1303248d7359af40c2f4a0a43654de3df0a..74fa8fbfcbdd7dcd58b3e19ae3947a9aa2c6209d 100644
--- a/tools/metaphlan2/metaphlan2/Snakefile
+++ b/tools/metaphlan2/metaphlan2/single/Snakefile
@@ -1,8 +1,10 @@
__metaphlan2_exec_command = config.get('metaphlan2', {}).get('exec_command', 'metaphlan2.py')
__metaphlan2_modules = config.get('metaphlan2', {}).get('modules')
+__metaphlan2_input_type = config['metaphlan2'].get('input_type', 'fastq')
__metaphlan2_options = config.get('metaphlan2', {}).get('options', "")
__metaphlan2_threads = config.get('metaphlan2', {}).get('threads', 1)
+
rule metaphlan2:
input:
__metaphlan2_input
@@ -12,6 +14,7 @@ rule metaphlan2:
exec_command = __metaphlan2_exec_command,
modules = __metaphlan2_modules,
input_type = __metaphlan2_input_type,
+ bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan2_output_dir, sample="{sample}"),
options = __metaphlan2_options
threads:
__metaphlan2_threads
@@ -19,5 +22,5 @@ rule metaphlan2:
command = []
if params.modules:
command.append("module load {params.modules}")
- command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} {params.options} {input} {output}")
+ command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} --bowtie2out {params.bowtie2out} {params.options} {input} {output}")
shell(" && ".join(command))
diff --git a/tools/metaphlan2/metaphlan2/config.yaml b/tools/metaphlan2/metaphlan2/single/config_example.yaml
similarity index 100%
rename from tools/metaphlan2/metaphlan2/config.yaml
rename to tools/metaphlan2/metaphlan2/single/config_example.yaml
diff --git a/tools/metaphlan2/metaphlan2/usage_example.rules b/tools/metaphlan2/metaphlan2/usage_example.rules
deleted file mode 100644
index b4e995a389fb71d7334433f8d9233c14ae38c96a..0000000000000000000000000000000000000000
--- a/tools/metaphlan2/metaphlan2/usage_example.rules
+++ /dev/null
@@ -1,26 +0,0 @@
-"""
-This example would be used as followed:
-
-$ snakemake --snakefile metaphlan2.rules output/s01.txt
-
-It requires the presence of data/s01.fastq.gz to work based on config file
-"""
-
-configfile: "config.yaml"
-
-__input_dir = config['input_dir']
-__main_output_dir = config.get('output_dir', 'output')
-
-# ---- Metaphlan2
-__metaphlan2_output_dir = __main_output_dir + "/metaphlan2"
-__metaphlan2_input_type = config['metaphlan2'].get('input_type', 'fastq')
-__metaphlan2_input = "{dir}/{sample}.{ext}".format(dir=__input_dir,
- sample="{sample}",
- ext=__metaphlan2_input_type + ".gz")
-__metaphlan2_output = "{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
- sample="{sample}")
-include: "Snakefile"
-
-rule all:
- input:
- __metaphlan2_output
diff --git a/workflows/README.md b/workflows/README.md
index e51a50f8c142c65b283372d31037c807dd204765..c2586a62e7568646bcf7d3239242073040f88165 100644
--- a/workflows/README.md
+++ b/workflows/README.md
@@ -13,6 +13,8 @@ Therefore, workflows have the following parts:
4. Set up of specific variables for the tools
5. `rule all` to specify what is/are the specific file(s) expected from the workflow.
+> **Note**: These workflows are not made to be fully portable and reusable but at least give around 80% of the work done. You might need to do minor modifications. The idea being to have a copy of `Snakefile` workflow with its dedicated `config.yaml` file for each experiments.
+
### Reference to options from `config.yaml` file
First part correspond to all options that are set up from a `config.yaml` file. They all have the nomenclature `__TOOLNAME_variable`.
diff --git a/workflows/metaphlan2/README.md b/workflows/metaphlan2/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..9535edaf2fde3aff6cf142a43553df7579822ad2
--- /dev/null
+++ b/workflows/metaphlan2/README.md
@@ -0,0 +1,8 @@
+# Simple metaphlan2 workflows
+
+Workflows using metaphlan2 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.
diff --git a/workflows/metaphlan2/paired_metaphlan2/Snakefile b/workflows/metaphlan2/paired_metaphlan2/Snakefile
new file mode 100644
index 0000000000000000000000000000000000000000..e8785568835c18fea5fc31f77b434f4a86e0866b
--- /dev/null
+++ b/workflows/metaphlan2/paired_metaphlan2/Snakefile
@@ -0,0 +1,58 @@
+configfile: "config.yaml"
+
+# ==== Snakefile paths ====
+__metaphlan2_rules = config.get("snakefiles", {}).get("metaphlan2", "../../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')
+
+# ---- Metaphlan2
+__metaphlan2_suffix = config['metaphlan2'].get('pair_suffix', '')
+__metaphlan2_output_dir = __main_output_dir + "/metaphlan2"
+__metaphlan2_input_type = config['metaphlan2'].get('input_type', 'fastq')
+__metaphlan2_input_r1 = "{dir}/{sample}_R1{suffix}.{ext}".format(dir=__input_dir,
+ sample="{sample}",
+ suffix=__metaphlan2_suffix,
+ ext=__metaphlan2_input_type + ".gz")
+__metaphlan2_input_r2 = "{dir}/{sample}_R2{suffix}.{ext}".format(dir=__input_dir,
+ sample="{sample}",
+ suffix=__metaphlan2_suffix,
+ ext=__metaphlan2_input_type + ".gz")
+__metaphlan2_output = "{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
+ sample="{sample}")
+include: __metaphlan2_rules
+
+# ---- Metaphlan2 merge
+__metaphlan2_merge_output_dir = __main_output_dir + "/metaphlan2_merge"
+__metaphlan2_merge_output_file_name = config['metaphlan2_merge'].get('output_file_name',"merged_taxonomic_profiles.txt")
+__metaphlan2_merge_input = expand("{dir}/{sample}.txt".format(dir=__metaphlan2_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
+
+# ---- 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',"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:
+ heatmap = __metaphlan2_heatmap_output,
+ dendogram = __graphlan_from_metaphlan2_output
+
diff --git a/workflows/metaphlan2/paired_metaphlan2/config.yaml b/workflows/metaphlan2/paired_metaphlan2/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..21b4cbde2f02258dc4727f8c7fb95bf64978f675
--- /dev/null
+++ b/workflows/metaphlan2/paired_metaphlan2/config.yaml
@@ -0,0 +1,44 @@
+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
+
+samples:
+ - sample_1
+ - sample_2
+ - sample_2
+
+input_dir: /a/path/to/input/data
+output_dir: metaphlan2_output
+
+metaphlan2:
+ modules: singularity
+ threads: 4
+ input_type: fastq
+ pair_suffix: "_001"
+ 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"
diff --git a/workflows/simple_metaphlan2/Snakefile b/workflows/metaphlan2/single_metaphlan2/Snakefile
similarity index 90%
rename from workflows/simple_metaphlan2/Snakefile
rename to workflows/metaphlan2/single_metaphlan2/Snakefile
index ba2059a1a193662baeb75a87c38a1cea97ffa8ee..413024e674a1c41c2a710827e289c6ee554931fe 100644
--- a/workflows/simple_metaphlan2/Snakefile
+++ b/workflows/metaphlan2/single_metaphlan2/Snakefile
@@ -1,10 +1,10 @@
configfile: "config.yaml"
# ==== Snakefile paths ====
-__metaphlan2_rules = config.get("snakefiles", {}).get("metaphlan2", "../../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")
+__metaphlan2_rules = config.get("snakefiles", {}).get("metaphlan2")
+__metaphlan2_merge_rules = config.get("snakefiles", {}).get("metaphlan2_merge")
+__metaphlan2_heatmap_rules = config.get("snakefiles", {}).get("metaphlan2_heatmap")
+__graphlan_from_metaphlan2_rules = config.get("snakefiles", {}).get("graphlan_from_metaphlan2")
__input_dir = config['input_dir']
__main_output_dir = config.get('output_dir', 'output')
diff --git a/workflows/metaphlan2/single_metaphlan2/config.yaml b/workflows/metaphlan2/single_metaphlan2/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..6d7b5bf0d573cee970a0122ca45ad7b0ea941363
--- /dev/null
+++ b/workflows/metaphlan2/single_metaphlan2/config.yaml
@@ -0,0 +1,43 @@
+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
+
+samples:
+ - sample_1
+ - sample_2
+ - sample_2
+
+input_dir: /a/path/to/input/data
+output_dir: metaphlan2_output
+
+metaphlan2:
+ 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"
diff --git a/workflows/simple_metaphlan2/README.md b/workflows/simple_metaphlan2/README.md
deleted file mode 100644
index 9014992dbf8ebef87732069302c816f3f37f152a..0000000000000000000000000000000000000000
--- a/workflows/simple_metaphlan2/README.md
+++ /dev/null
@@ -1,7 +0,0 @@
-# Simple metaphlan2 workflow
-
-This is a simple example of a workflow using metaphlan2.
-
-## Example
-
-An example is provided and is based on the `config.yaml` file. Singularity images are necessary for this example as well as the samples in the appropriate folder.
\ No newline at end of file
diff --git a/workflows/simple_metaphlan2/config.yaml b/workflows/simple_metaphlan2/config.yaml
deleted file mode 100644
index c8c0b9f99ca675a715e49aacbdc18dd8286bdfda..0000000000000000000000000000000000000000
--- a/workflows/simple_metaphlan2/config.yaml
+++ /dev/null
@@ -1,33 +0,0 @@
-samples:
- - SRS014459-Stool
- - SRS014464-Anterior_nares
- - SRS014470-Tongue_dorsum
- - SRS014472-Buccal_mucosa
- - SRS014476-Supragingival_plaque
- - SRS014494-Posterior_fornix
-
-input_dir: /pasteur/homes/kehillio/Atm/kenzo/repo/workflow-benchmarking/data
-output_dir: 20190509_simplecase
-
-metaphlan2:
- threads: 4
- input_type: fasta
- exec_command: singularity run --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/metaphlan2/metaphlan2.simg
-
-metaphlan2_merge:
- exec_command: singularity run --app merge --bind /pasteur/ /pasteur/gaia/projets/p01/Atm/singularity/metaphlan2/metaphlan2.simg
-
-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