Commit 8a7ec2e8 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

update paths from tars to maestro

parent 17767e09
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
......
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
......
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
......
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
......
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
......
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
......
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
......
......@@ -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}")
......
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