update paths from tars to maestro

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/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/paired_metaphlan2/Snakefile

@@ -13,11 +13,11 @@ __main_output_dir = config.get('output_dir', 'output')
 __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")
+                                                     sample="{sample}",
+                                                     ext="_1.fq.gz")
 __metaphlan3_input_r2 = "{dir}/{sample}{ext}".format(dir=__input_dir,
-                                                      sample="{sample}",
-                                                      ext="_2.fq.gz")
+                                                     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}")