Merge pull request #724 from maxplanck-ie/dev_ksikora2

Dev ksikora2
maxplanck-ie · Nov 16, 2020 · 788163a · 788163a
2 parents d5de621 + a60d1b9
commit 788163a
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diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.3.1
+  version: 2.4.0
 
 source:
   path: ../

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,14 +1,16 @@
 snakePipes News
 ===============
 
-snakePipes x.y.z
+snakePipes 2.4.0
 ----------------
 
 * Added support for multiple pairwise comparisons for DESeq2, sleuth, and rMats in the mRNA-seq workflow, as well as for DESeq2 in the noncoding-RNA-seq workflow.
 * Loompy from conda is now used in mode STARsolo in scRNA-seq workflow.
 * Added bamExt to mRNA-seq and noncoding-RNA-seq commandline arguments.
 * Added multi-thread support to rMats in mRNA-seq workflow.
 * Fixed deepTools GC bias command with SE reads.
+* Bumped HiC explorer version.
+* Fixed STARsoloCoords for Custom kit.
 
 
 snakePipes 2.3.1

diff --git a/docs/content/setting_up.rst b/docs/content/setting_up.rst
@@ -34,7 +34,7 @@ The easiest way to install snakePipes is via our conda channel. The following co
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.3.1
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.0
 
 This way, the software used within snakePipes do not conflict with the software pre-installed on your terminal or in your python environment.
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -34,7 +34,7 @@ Quick start
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.3.1
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.0
 
 * You can update snakePipes to the latest version available on conda with:
 

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.3.1'
+__version__ = '2.4.0'
diff --git a/snakePipes/workflows/scRNAseq/internals.snakefile b/snakePipes/workflows/scRNAseq/internals.snakefile
@@ -74,6 +74,7 @@ if mode == "STARsolo":
         if not os.path.isfile(BCwhiteList):
             print("Provided barcode whitelist file doesn't exist! Exit...\n")
             exit(1)
+        STARsoloCoords = STARsoloCoords.split(',')
 
 ## After barcode transfer to R2 we have only single end data / R2
 ## but we need to keep "reads" for rule fastq_barcode

diff --git a/snakePipes/workflows/scRNAseq/scRNAseq b/snakePipes/workflows/scRNAseq/scRNAseq
@@ -118,7 +118,7 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                           default=defaults["BCwhiteList"])
 
     optional.add_argument("--STARsoloCoords",
-                          type=list,
+                          type=str,
                           help="Comma-separated list of values: UMI start position, UMI length, CB start position, CB length. Required for the STARsolo mode (default: '%(default)s')",
                           default=defaults["STARsoloCoords"])