added the genome hg38

ucsd-ccbb · May 27, 2020 · e91b9a9 · e91b9a9
1 parent b893dc1
commit e91b9a9
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Showing 4 changed files with 4 additions and 3 deletions.
diff --git a/notebooks/cirrus-ngs/ChiPSeq Pipeline.ipynb b/notebooks/cirrus-ngs/ChiPSeq Pipeline.ipynb
@@ -94,7 +94,7 @@
     "#options: homer\n",
     "workflow = \"homer\"\n",
     "\n",
-    "#options: hg19, mm10\n",
+    "#options: hg38, hg19, mm10\n",
     "genome = \"hg19\"\n",
     "\n",
     "#options: factor, histone\n",

diff --git a/src/cirrus_ngs/server/Pipelines/config/ChiPSeq/ChiPSeq_homer.yaml b/src/cirrus_ngs/server/Pipelines/config/ChiPSeq/ChiPSeq_homer.yaml
@@ -29,7 +29,7 @@ align:
     script_path: "ChiPSeq/homer/bowtie"
     download_suffix: ".trim{}"
     input_is_output: True
-    can_be_zipped: False
+    can_be_zipped: True
     uses_chromosomes: False
     extra_bash_args:
         - 4     # number of threads

diff --git a/src/cirrus_ngs/server/Pipelines/config/software.conf b/src/cirrus_ngs/server/Pipelines/config/software.conf
@@ -45,6 +45,7 @@ export hg38_fasta="$reference_dir/Hsapiens/hg38/sequence/GRCh38.p12.genome.fa"
 export hg38_chromosome_list="chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chrM"
 export hg38_fai="$reference_dir/Hsapiens/hg38/sequence/GRCh38.p12.genome.fa.fai"
 export hg38_bwa_index="$reference_dir/Hsapiens/hg38/indices/bwa/GRCh38.p2.genome.fa"
+export hg38_bowtie_index="$reference_dir/Hsapiens/hg38/indices/bowtie/genome"
 export hg38_STAR_index="$reference_dir/Hsapiens/hg38/indices/RSEM"
 export hg38_gtf="$reference_dir/Hsapiens/hg38/annotations/gencode.v29.annotation.gtf"
 export hg38_rsem_index="$reference_dir/Hsapiens/hg38/indices/RSEM/RSEM"

diff --git a/src/cirrus_ngs/server/Pipelines/config/tools.yaml b/src/cirrus_ngs/server/Pipelines/config/tools.yaml
@@ -127,7 +127,7 @@ bowtie:
     script_path: "ChiPSeq/homer/bowtie"
     download_suffix: ".trim{}"
     input_is_output: True
-    can_be_zipped: False
+    can_be_zipped: True
     uses_chromosomes: False
 make_tag_directory:
     script_path: "ChiPSeq/homer/make_tag_directory"