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Metagenomics
snakemake
Commits
8a7ec2e8
Commit
8a7ec2e8
authored
Dec 14, 2020
by
Kenzo-Hugo Hillion
♻
Browse files
update paths from tars to maestro
parent
17767e09
Changes
8
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tools/eggnogmapper2/annotate/example_usage/config.yaml
View file @
8a7ec2e8
snakefiles
:
eggnogmapper2_annotate
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/eggnogmapper2/annotate/Snakefile
eggnogmapper2_annotate
:
/pasteur/
zeus/
projets/p
02/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
View file @
8a7ec2e8
snakefiles
:
eggnogmapper2_diamond
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/eggnogmapper2/diamond/Snakefile
eggnogmapper2_diamond
:
/pasteur/
zeus/
projets/p
02/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
View file @
8a7ec2e8
snakefiles
:
cat
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/utils/cat/Snakefile
cat
:
/pasteur/
zeus/
projets/p
02/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
View file @
8a7ec2e8
snakefiles
:
split_fasta
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/utils/split_fasta/Snakefile
split_fasta
:
/pasteur/
zeus/
projets/p
02/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
View file @
8a7ec2e8
snakefiles
:
eggnogmapper2_diamond
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/eggnogmapper2/diamond/Snakefile
split_fasta
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/utils/split_fasta/Snakefile
cat
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/utils/cat/Snakefile
eggnogmapper2_annotate
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/eggnogmapper2/annotate/Snakefile
eggnogmapper2_diamond
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/eggnogmapper2/diamond/Snakefile
split_fasta
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/utils/split_fasta/Snakefile
cat
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/utils/cat/Snakefile
eggnogmapper2_annotate
:
/pasteur/
zeus/
projets/p
02/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
View file @
8a7ec2e8
snakefiles
:
metaphlan2
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/metaphlan2/metaphlan2/paired/Snakefile
metaphlan2_merge
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
metaphlan2_heatmap
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/metaphlan2/metaphlan2_heatmap/Snakefile
graphlan_from_metaphlan2
:
/pasteur/projets/p
olicy01/Atm
/snakemake/subworkflows/graphlan_from_metaphlan2/Snakefile
metaphlan2
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/metaphlan2/metaphlan2/paired/Snakefile
metaphlan2_merge
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
metaphlan2_heatmap
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/metaphlan2/metaphlan2_heatmap/Snakefile
graphlan_from_metaphlan2
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/subworkflows/graphlan_from_metaphlan2/Snakefile
samples
:
-
sample_1
...
...
workflows/metaphlan2/single_metaphlan2/config.yaml
View file @
8a7ec2e8
snakefiles
:
metaphlan2
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/metaphlan2/metaphlan2/single/Snakefile
metaphlan2_merge
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
metaphlan2_heatmap
:
/pasteur/projets/p
olicy01/Atm
/snakemake/tools/metaphlan2/metaphlan2_heatmap/Snakefile
graphlan_from_metaphlan2
:
/pasteur/projets/p
olicy01/Atm
/snakemake/subworkflows/graphlan_from_metaphlan2/Snakefile
metaphlan2
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/metaphlan2/metaphlan2/single/Snakefile
metaphlan2_merge
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/metaphlan2/metaphlan2_merge/Snakefile
metaphlan2_heatmap
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/tools/metaphlan2/metaphlan2_heatmap/Snakefile
graphlan_from_metaphlan2
:
/pasteur/
zeus/
projets/p
02/metasig/gitlab
/snakemake/subworkflows/graphlan_from_metaphlan2/Snakefile
samples
:
-
sample_1
...
...
workflows/metaphlan3/paired_metaphlan2/Snakefile
View file @
8a7ec2e8
...
...
@@ -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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