Merge pull request #873 from maxplanck-ie/leily_mrna

changes in STAR command and version
maxplanck-ie · Jan 16, 2023 · 19f5b1d · 19f5b1d
2 parents efd4f8a + 31d4d66
commit 19f5b1d
Show file tree

Hide file tree

Showing 5 changed files with 10 additions and 7 deletions.
diff --git a/snakePipes/shared/rules/RNA_mapping.snakefile b/snakePipes/shared/rules/RNA_mapping.snakefile
@@ -123,7 +123,8 @@ elif aligner.upper().find("STAR") >=0:
                     --outStd BAM_Unsorted \
                     --sjdbGTFfile {params.gtf} \
                     --genomeDir {params.index} \
-                    --readFilesIn <(gunzip -c {input.r1}) <(gunzip -c {input.r2}) \
+                    --readFilesIn  {input.r1} {input.r2} \
+                    --readFilesCommand 'gunzip -c' \
                     --outFileNamePrefix {params.prefix} \
                 | samtools sort -m {params.samsort_memory} -T $MYTEMP/{wildcards.sample} -@ {params.samtools_threads} -O bam -o {output.bam} - 2> {log}
                 rm -rf $MYTEMP
@@ -160,7 +161,8 @@ elif aligner.upper().find("STAR") >=0:
                     --outStd BAM_Unsorted \
                     --sjdbGTFfile {params.gtf} \
                     --genomeDir {params.index} \
-                    --readFilesIn <(gunzip -c {input}) \
+                    --readFilesIn {input} \
+                    --readFilesCommand 'gunzip -c' \
                     --outFileNamePrefix {params.prefix} \
                 | samtools sort -m {params.samsort_memory} -T $MYTEMP/{wildcards.sample} -@ {params.samtools_threads} -O bam -o {output.bam} - 2> {log}
                 rm -rf $MYTEMP

diff --git a/snakePipes/shared/rules/envs/createIndices.yaml b/snakePipes/shared/rules/envs/createIndices.yaml
@@ -8,7 +8,7 @@ dependencies:
  - ucsc-genepredtobed
  - bowtie2 = 2.4.5
  - hisat2 = 2.2.1
- - star = 2.7.10a
+ - star = 2.7.10b
  - bwa = 0.7.17
  - bwa-mem2 = 2.2.1
  - bwameth = 0.2.5

diff --git a/snakePipes/shared/rules/envs/rna_seq.yaml b/snakePipes/shared/rules/envs/rna_seq.yaml
@@ -8,7 +8,7 @@ dependencies:
  - samtools = 1.15.1
  - subread = 2.0.1
  - hisat2 = 2.2.1
- - star = 2.7.10a
+ - star = 2.7.10b
  - salmon = 1.9.0
  - r-base = 4.1.3
  - r-wasabi

diff --git a/snakePipes/shared/rules/envs/sc_rna_seq.yaml b/snakePipes/shared/rules/envs/sc_rna_seq.yaml
@@ -5,12 +5,12 @@ channels:
 dependencies:
  - umi_tools = 1.1.2
  - samtools = 1.15.1
- - star = 2.7.10a
+ - star = 2.7.10b
  - r-base = 4.1.3
  - r-stringr
  - r-data.table
- - r-seurat = 4.1.1 
+ - r-seurat = 4.1.1
  - r-gtools
  - r-dplyr
  - h5py = 3.6.0
- - velocyto.py = 0.17.17 
+ - velocyto.py = 0.17.17
diff --git a/snakePipes/shared/rules/envs/shared.yaml b/snakePipes/shared/rules/envs/shared.yaml
@@ -3,6 +3,7 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
+ - python = 3.7.12 #This can be changed together with the update of deeptools to the next version
  - deeptools = 3.5.1
  - seqtk = 1.3
  - pigz = 2.6