Salmon_wasabi localrule and rm private env path

maxplanck-ie · Aug 9, 2019 · 9da7c37 · 9da7c37
1 parent 0247055
commit 9da7c37
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diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -11,6 +11,7 @@ snakePipes 1.2.3
  * ATACseq peakQC is now run on fragment-size filtered bam
  * Fixed Salmon output (Number of Reads output in "*counts.tsv" files and file naming)
  * Fixed CSAW QC plot error with single end reads
+ * Updated histone HMM environment to a working conda version
 
 snakePipes 1.2.2
 ----------------

diff --git a/snakePipes/shared/defaults.yaml b/snakePipes/shared/defaults.yaml
@@ -6,8 +6,7 @@
 # Note that due to limitations in yaml.dump, only very basic structures are
 # permitted here.
 ################################################################################
-#snakemake_options: ' --use-conda --conda-prefix /package/anaconda3/envs/ '
-snakemake_options: '--use-conda --conda-prefix /data/processing/sikora/snakePipes_envs'
+snakemake_options: ' --use-conda --conda-prefix /package/anaconda3/envs/ '
 tempdir: /data/extended/
 # The following are only needed if you use the --emailAddress option
 smtpServer:

diff --git a/snakePipes/workflows/RNA-seq/Snakefile b/snakePipes/workflows/RNA-seq/Snakefile
@@ -269,7 +269,7 @@ onstart:
 ################################################################################
 
 if not fromBam:
-    localrules: FASTQ1, FASTQ2
+    localrules: FASTQ1, FASTQ2, Salmon_wasabi
 
     rule all:
         input:
@@ -288,6 +288,8 @@ if not fromBam:
             "multiQC/multiqc_report.html"
 
 else:
+    localrules: Salmon_wasabi
+
     rule all:
         input:
             "Annotation/genes.annotated.bed",