Merge pull request #714 from maxplanck-ie/dev_ksikora2

Misc
maxplanck-ie · Oct 22, 2020 · 1f8fe1f · 1f8fe1f
2 parents 2e9b66f + a2ad4cc
commit 1f8fe1f
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diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,6 +1,12 @@
 snakePipes News
 ===============
 
+snakePipes x.y.z
+----------------
+
+* Loompy from conda is now used in mode STARsolo in scRNA-seq workflow.
+* Added bamExt to mRNA-seq and noncoding-RNA-seq commandline arguments.
+
 snakePipes 2.3.1
 ----------------
 

diff --git a/snakePipes/shared/rules/envs/sc_rna_seq_loompy.yaml b/snakePipes/shared/rules/envs/sc_rna_seq_loompy.yaml
@@ -4,5 +4,4 @@ channels:
  - bioconda
 dependencies:
  - python=3.8
- - pip:
-   - loompy
+ - loompy=3.0.6
diff --git a/snakePipes/workflows/mRNA-seq/mRNA-seq b/snakePipes/workflows/mRNA-seq/mRNA-seq
@@ -28,7 +28,7 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                          "filterGTF": None, "sampleSheet": None,
                          "reads": ["_R1", "_R2"], "ext": ".fastq.gz",
                          "bwBinSize": 25, "dnaContam": False, "plotFormat": "png",
-                         "fromBAM": False, "pairedEnd": True,
+                         "fromBAM": False, "bamExt": ".bam", "pairedEnd": True,
                          "UMIDedup": False,
                          "UMIDedupOpts": "", "bcPattern": "NNNNCCCCCCCCC",
                          "UMIDedupSep": "_", "UMIBarcode": False, "rMats": False}):
@@ -103,6 +103,11 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                          help="Input folder with bam files. If provided, the analysis will start from this point. If bam files contain single ends, please specify --singleEnd additionally.",
                          default=defaults["fromBAM"])
 
+    optional.add_argument("--bamExt",
+                          help="Extention of provided bam files, will be substracted from basenames to obtain sample names. (default: '%(default)s')",
+                          default=defaults["bamExt"])
+
+
     optional.add_argument("--singleEnd",
                           dest="pairedEnd",
                           action="store_false",

diff --git a/snakePipes/workflows/noncoding-RNA-seq/noncoding-RNA-seq b/snakePipes/workflows/noncoding-RNA-seq/noncoding-RNA-seq
@@ -27,7 +27,7 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                          "sampleSheet": None,
                          "reads": ["_R1", "_R2"], "ext": ".fastq.gz",
                          "bwBinSize": 25, "plotFormat": "png",
-                         "fromBAM": False, "pairedEnd": True,
+                         "fromBAM": False, "bamExt": ".bam", "pairedEnd": True,
                          "UMIDedup": False,
                          "UMIDedupOpts": "", "bcPattern": "NNNNCCCCCCCCC",
                          "UMIDedupSep": "_", "UMIBarcode": False}):
@@ -76,6 +76,11 @@ def parse_args(defaults={"verbose": False, "configFile": None,
                          help="Input folder with bam files. If provided, the analysis will start from this point. If bam files contain single ends, please specify --singleEnd additionally.",
                          default=defaults["fromBAM"])
 
+    optional.add_argument("--bamExt",
+                          help="Extention of provided bam files, will be substracted from basenames to obtain sample names. (default: '%(default)s')",
+                          default=defaults["bamExt"])
+
+
     optional.add_argument("--singleEnd",
                           dest="pairedEnd",
                           action="store_false",