🇨🇳 release v0.5.2

v0.5.2-b

celseq2/qc.py

@@ -84,12 +84,12 @@ def plotly_qc(fpath, saveto, sep=',', name=''):
 
     total_num_UMIs = expr.sum(axis=0)
     num_detected_genes = (expr > 0).sum(axis=0)
-    mt_index = pd.Series(
-        [x for x in expr.index if x.startswith('mt-') or x.startswith('MT-')])
+    mt_index = [x for x in expr.index if x.startswith(
+        'mt-') or x.startswith('MT-')]
     if not mt_index:
         percent_mt = 0
     else:
-        mt_umis = expr.loc[mt_index, :].sum(axis=0)
+        mt_umis = expr.loc[pd.Series(mt_index), :].sum(axis=0)
         percent_mt = mt_umis / total_num_UMIs
         percent_mt = percent_mt.replace(np.inf, 0)
 

celseq2/template/config.yaml

@@ -23,6 +23,10 @@ STAR: '/absolute/path/to/star'
 ## Whare is the directory to save STAR index?
 STAR_INDEX_DIR: '/absolute/path/to/star/folder/'
 
+## Extra parameters to run aligner. For example:
+## '--outSAMmultNmax 1 --outFilterScoreMinOverLread 0.3'
+ALIGNER_EXTRA_PARAMETERS: ''
+
 ####################################
 ## Annotations ##
 ####################################

celseq2/workflow/celseq2_beta.snakemake

@@ -43,6 +43,8 @@ BOWTIE2_INDEX_PREFIX = config.get('BOWTIE2_INDEX_PREFIX', None)
 BOWTIE2 = config.get('BOWTIE2', None)  # '/local/apps/bowtie2/2.3.1/bowtie2'
 STAR_INDEX_DIR = config.get('STAR_INDEX_DIR', None)
 STAR = config.get('STAR', None)
+ALIGNER_EXTRA_PARAMETERS = config.get('ALIGNER_EXTRA_PARAMETERS', '')
+
 ## Annotations ##
 # '/ifs/data/yanailab/refs/danio_rerio/danRer10_87/gtf/Danio_rerio.GRCz10.87.gtf.gz'
 GFF = config.get('GFF', None)
@@ -345,20 +347,21 @@ if ALIGNER == 'bowtie2':
             sam = join_path(DIR_PROJ, SUBDIR_ALIGN_ITEM,
                             '{itemID}', ALIGNER+'.bigsam'),
         params:
-            threads = num_threads
+            threads = num_threads,
+            aligner_extra_parameters = ALIGNER_EXTRA_PARAMETERS,
         log:
             join_path(DIR_PROJ, SUBDIR_LOG, '{itemID}',
                       'Align-Bowtie2.log')
         run:
-            shell(
-                """
-                {BOWTIE2} \
-                -p {params.threads} \
-                -x {BOWTIE2_INDEX_PREFIX} \
-                -U {input.fq} \
-                -S {output.sam} 2>{log} \
-                --seed 42
-                """)
+            cmd = '{BOWTIE2} '
+            cmd += '-p {params.threads} '
+            cmd += '-x {BOWTIE2_INDEX_PREFIX} '
+            cmd += '-U {input.fq} '
+            cmd += '-S {output.sam} '
+            cmd += '--seed 42 '
+            cmd += '{params.aligner_extra_parameters} '
+            cmd += '2>{log} '
+            shell(cmd)
 
 if ALIGNER == 'star':
     rule align_star:
@@ -377,9 +380,10 @@ if ALIGNER == 'star':
             star_prefix = join_path(DIR_PROJ, SUBDIR_ALIGN_ITEM,
                                     '{itemID}', '.star', ''),
             threads = num_threads,
+            aligner_extra_parameters = ALIGNER_EXTRA_PARAMETERS,
         run:
             mkfolder(params.star_prefix)
-            cmd = 'STAR '
+            cmd = '{STAR} '
             cmd += ' --runRNGseed 42 '
             cmd += ' --genomeLoad NoSharedMemory '
             cmd += ' --runThreadN {params.threads} '
@@ -388,6 +392,7 @@ if ALIGNER == 'star':
             cmd += ' --readFilesIn {input.fq} '
             cmd += ' --outFileNamePrefix {params.star_prefix} '
             # cmd += ' --outSAMmultNmax 1 '
+            cmd += ' {params.aligner_extra_parameters} '
             shell(cmd)
 
             starsam = join_path(params.star_prefix, 'Aligned.out.sam')

docs/about/release_note.md

@@ -10,6 +10,17 @@
 
 ---
 
+## :fa-flag-checkered: **v0.5.2**
+
+:fa-calendar: **2018-04-16**
+
+:fa-star: **Features**
+
+- Generate QC plots for UMI-counts matrices. If ST is performed, an extra QC plot masked on grid is generated.
+- Allow experienced users to feed extra parameters to align. See issue #10.
+
+---
+
 ## :fa-flag-checkered: **v0.5.1**
 
 :fa-calendar: **2018-04-05**