From a8449152c5b94fad557f2ec0d107fc99cd123483 Mon Sep 17 00:00:00 2001
From: hlopezma <hlopezma@pasteur.fr>
Date: Thu, 8 Sep 2022 14:24:14 +0200
Subject: [PATCH] conda ok

---
 workflow/rules/bamCoverage.rules                 | 2 +-
 workflow/rules/cutadapt.rules                    | 2 +-
 {envs => workflow/rules/envs}/bowtie2.yaml       | 0
 {envs => workflow/rules/envs}/cutadapt.yaml      | 0
 {envs => workflow/rules/envs}/deeptools.yaml     | 0
 {envs => workflow/rules/envs}/fastqc.yaml        | 0
 {envs => workflow/rules/envs}/featureCounts.yaml | 0
 {envs => workflow/rules/envs}/idr.yaml           | 0
 {envs => workflow/rules/envs}/macs2.yaml         | 0
 {envs => workflow/rules/envs}/multiqc.yaml       | 0
 {envs => workflow/rules/envs}/picard.yaml        | 0
 {envs => workflow/rules/envs}/pysam.yaml         | 0
 {envs => workflow/rules/envs}/samtools.yaml      | 0
 {envs => workflow/rules/envs}/seacr.yaml         | 0
 {envs => workflow/rules/envs}/spp.yaml           | 0
 15 files changed, 2 insertions(+), 2 deletions(-)
 rename {envs => workflow/rules/envs}/bowtie2.yaml (100%)
 rename {envs => workflow/rules/envs}/cutadapt.yaml (100%)
 rename {envs => workflow/rules/envs}/deeptools.yaml (100%)
 rename {envs => workflow/rules/envs}/fastqc.yaml (100%)
 rename {envs => workflow/rules/envs}/featureCounts.yaml (100%)
 rename {envs => workflow/rules/envs}/idr.yaml (100%)
 rename {envs => workflow/rules/envs}/macs2.yaml (100%)
 rename {envs => workflow/rules/envs}/multiqc.yaml (100%)
 rename {envs => workflow/rules/envs}/picard.yaml (100%)
 rename {envs => workflow/rules/envs}/pysam.yaml (100%)
 rename {envs => workflow/rules/envs}/samtools.yaml (100%)
 rename {envs => workflow/rules/envs}/seacr.yaml (100%)
 rename {envs => workflow/rules/envs}/spp.yaml (100%)

diff --git a/workflow/rules/bamCoverage.rules b/workflow/rules/bamCoverage.rules
index 87756b0..7c8375a 100755
--- a/workflow/rules/bamCoverage.rules
+++ b/workflow/rules/bamCoverage.rules
@@ -33,7 +33,7 @@ rule bamCoverage:
     singularity:
         "epeak.img"
     conda:
-        "envs/deeptools.yalm"
+        "envs/deeptools.yaml"
     params:
         options = bamCoverage_options
     envmodules:
diff --git a/workflow/rules/cutadapt.rules b/workflow/rules/cutadapt.rules
index 1ef341e..7d1ffa2 100755
--- a/workflow/rules/cutadapt.rules
+++ b/workflow/rules/cutadapt.rules
@@ -37,7 +37,7 @@ rule cutadapt:
     singularity:
         "epeak.img"
     conda:
-        envs/cutadapt.yaml
+        "envs/cutadapt.yaml"
     threads: config['adapters']['threads']
     log:
         out = cutadapt_log
diff --git a/envs/bowtie2.yaml b/workflow/rules/envs/bowtie2.yaml
similarity index 100%
rename from envs/bowtie2.yaml
rename to workflow/rules/envs/bowtie2.yaml
diff --git a/envs/cutadapt.yaml b/workflow/rules/envs/cutadapt.yaml
similarity index 100%
rename from envs/cutadapt.yaml
rename to workflow/rules/envs/cutadapt.yaml
diff --git a/envs/deeptools.yaml b/workflow/rules/envs/deeptools.yaml
similarity index 100%
rename from envs/deeptools.yaml
rename to workflow/rules/envs/deeptools.yaml
diff --git a/envs/fastqc.yaml b/workflow/rules/envs/fastqc.yaml
similarity index 100%
rename from envs/fastqc.yaml
rename to workflow/rules/envs/fastqc.yaml
diff --git a/envs/featureCounts.yaml b/workflow/rules/envs/featureCounts.yaml
similarity index 100%
rename from envs/featureCounts.yaml
rename to workflow/rules/envs/featureCounts.yaml
diff --git a/envs/idr.yaml b/workflow/rules/envs/idr.yaml
similarity index 100%
rename from envs/idr.yaml
rename to workflow/rules/envs/idr.yaml
diff --git a/envs/macs2.yaml b/workflow/rules/envs/macs2.yaml
similarity index 100%
rename from envs/macs2.yaml
rename to workflow/rules/envs/macs2.yaml
diff --git a/envs/multiqc.yaml b/workflow/rules/envs/multiqc.yaml
similarity index 100%
rename from envs/multiqc.yaml
rename to workflow/rules/envs/multiqc.yaml
diff --git a/envs/picard.yaml b/workflow/rules/envs/picard.yaml
similarity index 100%
rename from envs/picard.yaml
rename to workflow/rules/envs/picard.yaml
diff --git a/envs/pysam.yaml b/workflow/rules/envs/pysam.yaml
similarity index 100%
rename from envs/pysam.yaml
rename to workflow/rules/envs/pysam.yaml
diff --git a/envs/samtools.yaml b/workflow/rules/envs/samtools.yaml
similarity index 100%
rename from envs/samtools.yaml
rename to workflow/rules/envs/samtools.yaml
diff --git a/envs/seacr.yaml b/workflow/rules/envs/seacr.yaml
similarity index 100%
rename from envs/seacr.yaml
rename to workflow/rules/envs/seacr.yaml
diff --git a/envs/spp.yaml b/workflow/rules/envs/spp.yaml
similarity index 100%
rename from envs/spp.yaml
rename to workflow/rules/envs/spp.yaml
-- 
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