diff --git a/tools/eggnogmapper2/annotate/example_usage/config.yaml b/tools/eggnogmapper2/annotate/example_usage/config.yaml
index c7db75de9db3189ffa55b7a30aeb8813d1c34708..8e808da3b2b881ad7bb0afd4c8f178958c33c116 100644
--- a/tools/eggnogmapper2/annotate/example_usage/config.yaml
+++ b/tools/eggnogmapper2/annotate/example_usage/config.yaml
@@ -1,5 +1,5 @@
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
diff --git a/tools/eggnogmapper2/diamond/example_usage/config.yaml b/tools/eggnogmapper2/diamond/example_usage/config.yaml
index 5fe001f10aaab0b262680238247ff6684e7a9f5f..1db91027434c1c5e55d0f5d25f6ab5f9131b07b3 100644
--- a/tools/eggnogmapper2/diamond/example_usage/config.yaml
+++ b/tools/eggnogmapper2/diamond/example_usage/config.yaml
@@ -1,5 +1,5 @@
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
diff --git a/tools/metaphlan3/metaphlan/paired/Snakefile b/tools/metaphlan3/metaphlan/paired/Snakefile
index 55175901ad8cbe8aeb75453808d1b82196aa7810..87f4be7df06dcb1039952d068ae2e1d81500f668 100644
--- a/tools/metaphlan3/metaphlan/paired/Snakefile
+++ b/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:
diff --git a/tools/strainphlan/extract_markers/README.md b/tools/strainphlan/extract_markers/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..373182160daebbe4aadf5fee8848d999a25a8317
--- /dev/null
+++ b/tools/strainphlan/extract_markers/README.md
@@ -0,0 +1,18 @@
+# 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
+```
diff --git a/tools/strainphlan/sample2markers/README.md b/tools/strainphlan/sample2markers/README.md
index 8ef1f3bc248135cc747226d5935e2cbd48388886..78053e7abaa77d06229244c7f000712d9b8885dd 100644
--- a/tools/strainphlan/sample2markers/README.md
+++ b/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
```
diff --git a/tools/strainphlan/strainphlan/README.md b/tools/strainphlan/strainphlan/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..9def2825e4ce9f25194e863b5a743ac42bae0a77
--- /dev/null
+++ b/tools/strainphlan/strainphlan/README.md
@@ -0,0 +1,69 @@
+# 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)
+```
diff --git a/tools/strainphlan/strainphlan/Snakefile b/tools/strainphlan/strainphlan/Snakefile
new file mode 100644
index 0000000000000000000000000000000000000000..bf6d4effd2eb379e47496aa2666a4ce357421b2e
--- /dev/null
+++ b/tools/strainphlan/strainphlan/Snakefile
@@ -0,0 +1,25 @@
+__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))
diff --git a/tools/strainphlan/strainphlan/config.yaml b/tools/strainphlan/strainphlan/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..9094c16763ca77b1005040ca87affe372d2f64e7
--- /dev/null
+++ b/tools/strainphlan/strainphlan/config.yaml
@@ -0,0 +1,5 @@
+input_dir: data
+
+strainphlan:
+ threads: 4
+ exec_command: sample2markers.py
diff --git a/tools/utils/cat/example_usage/config.yaml b/tools/utils/cat/example_usage/config.yaml
index b0d0444ad73e58f3c1e6ebdde07204907fb38d95..fc1b43bf52c773c5974c1461092232cc4382b753 100644
--- a/tools/utils/cat/example_usage/config.yaml
+++ b/tools/utils/cat/example_usage/config.yaml
@@ -1,5 +1,5 @@
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
diff --git a/tools/utils/split_fasta/example_usage/config.yaml b/tools/utils/split_fasta/example_usage/config.yaml
index 559a78914eed47dc84b3382b4e651ad793500dcb..6b47f0307f8fd3e60d0f03be8a11023c5d198d6e 100644
--- a/tools/utils/split_fasta/example_usage/config.yaml
+++ b/tools/utils/split_fasta/example_usage/config.yaml
@@ -1,5 +1,5 @@
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
diff --git a/workflows/eggnogmapperv2/config.yaml b/workflows/eggnogmapperv2/config.yaml
index 10bd4b1ef1e47f342d64ab38b703e4c292be6d56..4e3f44d53646c5bd929560746f479956a1684b73 100644
--- a/workflows/eggnogmapperv2/config.yaml
+++ b/workflows/eggnogmapperv2/config.yaml
@@ -1,8 +1,8 @@
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
diff --git a/workflows/metaphlan2/paired_metaphlan2/config.yaml b/workflows/metaphlan2/paired_metaphlan2/config.yaml
index 21b4cbde2f02258dc4727f8c7fb95bf64978f675..077607ac5800b5d0d208ed5a185ae1c577b5a09f 100644
--- a/workflows/metaphlan2/paired_metaphlan2/config.yaml
+++ b/workflows/metaphlan2/paired_metaphlan2/config.yaml
@@ -1,8 +1,8 @@
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
diff --git a/workflows/metaphlan2/single_metaphlan2/config.yaml b/workflows/metaphlan2/single_metaphlan2/config.yaml
index 6d7b5bf0d573cee970a0122ca45ad7b0ea941363..3d5dccc54ba33a3ec9e846d4dcd2812b383ea610 100644
--- a/workflows/metaphlan2/single_metaphlan2/config.yaml
+++ b/workflows/metaphlan2/single_metaphlan2/config.yaml
@@ -1,8 +1,8 @@
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
diff --git a/workflows/metaphlan3/README.md b/workflows/metaphlan3/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..d1dc622811d5afaaa9d0b68b0fe592de77a0cfbb
--- /dev/null
+++ b/workflows/metaphlan3/README.md
@@ -0,0 +1,8 @@
+# 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.
diff --git a/workflows/metaphlan3/paired_metaphlan2/Snakefile b/workflows/metaphlan3/paired_metaphlan2/Snakefile
new file mode 100644
index 0000000000000000000000000000000000000000..eecd4a4be184e070d0ac47a1ccced07e3eb9dafb
--- /dev/null
+++ b/workflows/metaphlan3/paired_metaphlan2/Snakefile
@@ -0,0 +1,56 @@
+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
+
diff --git a/workflows/metaphlan3/paired_metaphlan2/config.yaml b/workflows/metaphlan3/paired_metaphlan2/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..3f6af03fe172edc2f49883dc7477e760b3a52646
--- /dev/null
+++ b/workflows/metaphlan3/paired_metaphlan2/config.yaml
@@ -0,0 +1,43 @@
+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"
diff --git a/workflows/strainphlan/README.md b/workflows/strainphlan/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..1bd172722b8e94154abf164bd65b4a540883bf9e
--- /dev/null
+++ b/workflows/strainphlan/README.md
@@ -0,0 +1,9 @@
+# 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
diff --git a/workflows/strainphlan/Snakefile b/workflows/strainphlan/Snakefile
new file mode 100644
index 0000000000000000000000000000000000000000..f7eb095548c619bebdecbea7b0a7356b4a260726
--- /dev/null
+++ b/workflows/strainphlan/Snakefile
@@ -0,0 +1,78 @@
+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'])
diff --git a/workflows/strainphlan/config.yaml b/workflows/strainphlan/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..788a77d9f2627a9c54b18ca6c6e95102ea813210
--- /dev/null
+++ b/workflows/strainphlan/config.yaml
@@ -0,0 +1,31 @@
+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