From 8a7ec2e8a4101f8b88d088dcc2bd4903829ae944 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@gmail.com>
Date: Mon, 14 Dec 2020 14:48:22 +0100
Subject: [PATCH] update paths from tars to maestro
---
tools/eggnogmapper2/annotate/example_usage/config.yaml | 2 +-
tools/eggnogmapper2/diamond/example_usage/config.yaml | 2 +-
tools/utils/cat/example_usage/config.yaml | 2 +-
tools/utils/split_fasta/example_usage/config.yaml | 2 +-
workflows/eggnogmapperv2/config.yaml | 8 ++++----
workflows/metaphlan2/paired_metaphlan2/config.yaml | 8 ++++----
workflows/metaphlan2/single_metaphlan2/config.yaml | 8 ++++----
workflows/metaphlan3/paired_metaphlan2/Snakefile | 8 ++++----
8 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/tools/eggnogmapper2/annotate/example_usage/config.yaml b/tools/eggnogmapper2/annotate/example_usage/config.yaml
index c7db75d..8e808da 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 5fe001f..1db9102 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/utils/cat/example_usage/config.yaml b/tools/utils/cat/example_usage/config.yaml
index b0d0444..fc1b43b 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 559a789..6b47f03 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 10bd4b1..4e3f44d 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 21b4cbd..077607a 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 6d7b5bf..3d5dccc 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/paired_metaphlan2/Snakefile b/workflows/metaphlan3/paired_metaphlan2/Snakefile
index 914d5c8..eecd4a4 100644
--- a/workflows/metaphlan3/paired_metaphlan2/Snakefile
+++ b/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}")
--
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