move relaxed alignment parameters for illumina to chemistry.json

rnabioco · Aug 28, 2024 · 2dfdaf0 · 2dfdaf0
1 parent 22de723
commit 2dfdaf0
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Showing 2 changed files with 6 additions and 12 deletions.
diff --git a/chemistry.yaml b/chemistry.yaml
@@ -1,7 +1,7 @@
 chromiumV3_illumina:
   filter_R1_length: 58
   bc_cut: ""
-  STAR_R1: "[WHITELIST_V3,\"--soloUMIlen 12 --clip5pNbases 58 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17\"]"
+  STAR_R1: "[WHITELIST_V3,\"--soloUMIlen 12 --clip5pNbases 58 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2\"]"
   STAR_R2: "[WHITELIST_V3,\"--soloUMIlen 12\"]"
   STAR_paired: "--alignEndsProtrude 58 ConcordantPair"
 chromiumV3_element:
@@ -17,31 +17,31 @@ chromiumV3_ultima:
 chromiumV2_illumina:
   filter_R1_length: 56
   bc_cut: ""
-  STAR_R1: "[WHITELIST_V2,\"--soloUMIlen 10 --clip5pNbases 56 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17\"]"
+  STAR_R1: "[WHITELIST_V2,\"--soloUMIlen 10 --clip5pNbases 56 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2\"]"
   STAR_R2: "[WHITELIST_V2,\"--soloUMIlen 10\"]"
   STAR_paired: "--alignEndsProtrude 56 ConcordantPair"
 dropseq_illumina:
   filter_R1_length: 50
   bc_cut: ""
-  STAR_R1: "None --soloUMIlen 8 --clip5pNbases 50 0 --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13"
+  STAR_R1: "None --soloUMIlen 8 --clip5pNbases 50 0 --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2"
   STAR_R2: "None --soloUMIlen 8 --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13"
   STAR_paired: "--alignEndsProtrude 50 ConcordantPair"
 microwellseq_illumina:
   filter_R1_length: 54
   bc_cut: "CGACTCACTACAGGG...TCGGTGACACGATCG"
-  STAR_R1: "None --soloUMIlen 6 --clip5pNbases 54 0 --soloCBstart 1 --soloCBlen 18 --soloUMIstart 19"
+  STAR_R1: "None --soloUMIlen 6 --clip5pNbases 54 0 --soloCBstart 1 --soloCBlen 18 --soloUMIstart 19 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2"
   STAR_R2: "None --soloUMIlen 6 --soloCBstart 1 --soloCBlen 18 --soloUMIstart 19"
   STAR_paired: "--alignEndsProtrude 54 ConcordantPair"
 bd_illumina:
   filter_R1_length: 53
   bc_cut: "ACTGGCCTGCGA...GGTAGCGGTGACA"
-  STAR_R1: "None --soloUMIlen 8 --clip5pNbases 53 0 --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28"
+  STAR_R1: "None --soloUMIlen 8 --clip5pNbases 53 0 --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2"
   STAR_R2: "None --soloUMIlen 8 --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28"
   STAR_paired: "--alignEndsProtrude 53 ConcordantPair"
 indrop_illumina:
   filter_R1_length: 32
   bc_cut: ""
-  STAR_R1: "None --soloUMIlen 6 --clip5pNbases 32 0 --soloCBstart 1 --soloCBlen 8 --soloUMIstart 9"
+  STAR_R1: "None --soloUMIlen 6 --clip5pNbases 32 0 --soloCBstart 1 --soloCBlen 8 --soloUMIstart 9 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2"
   STAR_R2: "None --soloUMIlen 6 --soloCBstart 1 --soloCBlen 8 --soloUMIstart 9"
   STAR_paired: "--alignEndsProtrude 32 ConcordantPair"
 
diff --git a/rules/cutadapt_star.snake b/rules/cutadapt_star.snake
@@ -153,9 +153,6 @@ rule starsolo_R1:
       --soloCBwhitelist {params.chemistry} \
       --soloBarcodeMate 1 \
       --soloStrand Reverse \
-      --outFilterMultimapNmax 1 \
-      --outFilterMismatchNmax 999 \
-      --outFilterMismatchNoverReadLmax 0.2 \
       --genomeDir {STAR_INDEX} \
       --soloFeatures Gene \
       --alignMatesGapMax 100000 \
@@ -240,9 +237,6 @@ rule starsolo_paired:
       {params.star_args_paired} \
       --soloBarcodeMate 1 \
       --soloStrand Reverse \
-      --outFilterMultimapNmax 1 \
-      --outFilterMismatchNmax 999 \
-      --outFilterMismatchNoverReadLmax 0.2 \
       --genomeDir {STAR_INDEX} \
       --soloFeatures Gene \
       --alignMatesGapMax 100000 \