Merge pull request #111 from baigal628/master

New Release for v1.3.2

MAESTRO/Snakemake/multi_scATAC/rules/sc_atac_peak_count_batch.smk

@@ -38,7 +38,7 @@ rule scatac_countpeak_batch:
     input:
         finalpeak = "Result/Analysis/Batch/all_samples_peaks.bed",
         validbarcode = "Result/QC/{sample}/{sample}_scATAC_validcells.txt",
-        frag = get_fragments
+        frag = "Result/minimap2/{sample}/fragments_corrected_dedup_count.tsv"
     output:
         counts = "Result/Analysis/Batch/{sample}/{sample}_peak_count.h5"
     params:

README.md

@@ -88,7 +88,7 @@ $ conda config --add channels bioconda
 $ conda config --add channels conda-forge
 # To make the installation faster, we recommend using mamba
 $ conda install mamba -c conda-forge
-$ mamba create -n MAESTRO maestro=1.3.1 -c liulab-dfci
+$ mamba create -n MAESTRO maestro=1.3.2 -c liulab-dfci
 # Activate the environment
 $ conda activate MAESTRO
 ```

conda/MAESTRO/meta.yaml

@@ -19,12 +19,12 @@ requirements:
     - snakemake >=5.14
     - rseqc >=3.0.0
     - star =2.7.6a
-    - minimap2 >=2.17
-    - samtools >=1.9
-    - bedtools >=2.29.2
+    - minimap2 =2.17
+    - samtools =1.10
+    - bedtools =2.29.2
     - rsem >=1.3.2
     - picard >=2.22.0
-    - macs2 >=2.2.6
+    - macs2 =2.2.7.1
     - lisa2 =2.2.2
     - umap-learn
     - pysam # this is needed by sinto
@@ -86,13 +86,13 @@ requirements:
     - snakemake >=5.14
     - rseqc >=3.0.0
     - star =2.7.6a
-    - minimap2 >=2.17
-    - samtools >=1.9
-    - bedtools >=2.29.2
+    - minimap2 =2.17
+    - samtools =1.10
+    - bedtools =2.29.2
     - rsem >=1.3.2
     - picard >=2.22.0
-    - macs2 >=2.2.6
-    - lisa2 >=2.1.0
+    - macs2 =2.2.7.1
+    - lisa2 =2.2.2
     - umap-learn
     - pysam # this is needed by sinto
     - r-base >=4.0.2