update chemistry confif to separate chemistry and platform

rnabioco · Sep 13, 2024 · 146b095 · 146b095
1 parent 4480512
commit 146b095
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Showing 3 changed files with 82 additions and 42 deletions.
diff --git a/Snakefile b/Snakefile
@@ -23,10 +23,31 @@ def _get_config(sample, item):
   try:
     return SAMPLES[sample][item]
   except KeyError:
-    try:
-      return CHEMISTRY[SAMPLES[sample]["chemistry"]][item]
-    except KeyError:
-      return DEFAULTS[item]
+    pass
+  try:
+    return CHEMISTRY[SAMPLES[sample]["chemistry"]][SAMPLES[sample]["platform"]][item]
+  except KeyError:
+    pass
+  try:
+    return CHEMISTRY[SAMPLES[sample]["chemistry"]][DEFAULTS["platform"]][item]
+  except KeyError:
+    pass
+  try:
+    return CHEMISTRY[SAMPLES[sample]["chemistry"]][item]
+  except KeyError:
+    pass
+  try:
+    return CHEMISTRY[DEFAULTS["chemistry"]][SAMPLES[sample]["platform"]][item]
+  except KeyError:
+    pass
+  try:
+    return CHEMISTRY[DEFAULTS["chemistry"]][DEFAULTS["platform"]][item]
+  except KeyError:
+    pass
+  try:
+    return CHEMISTRY[DEFAULTS["chemistry"]][item]
+  except KeyError:
+    return DEFAULTS[item]
 
 # assemble outputs for rule all
 SAMPLE_OUTS = []

diff --git a/chemistry.yaml b/chemistry.yaml
@@ -1,38 +1,53 @@
-chromiumV3_illumina:
-  filter_R1_length: 58
+# Chemistry and platform-specific configurations
+#
+# Example:
+#
+# chemistry1:
+#   platform_agnostic_option1: ...
+#   platform_agnostic_option2: ...
+#   name_of_platform1:
+#     filter_R1_length: ...
+#     STAR_R1: ...
+#     STAR_R2: ...
+
+chromiumV3:
   bc_whitelist: WHITELIST_V3
-  STAR_R1: --soloUMIlen 12 --clip5pNbases 58 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
-  STAR_R2: --soloUMIlen 12
-chromiumV3_element:
-  filter_R1_length: False
-  bc_whitelist: WHITELIST_V3
-  STAR_R1: --soloUMIlen 12 --clip5pNbases 48 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17
-  STAR_R2: --soloUMIlen 12
-chromiumV3_ultima:
-  filter_R1_length: 58
-  bc_whitelist: WHITELIST_V3
-  STAR_R1: --soloUMIlen 9 --clip5pNbases 58 --soloCBstart 23 --soloCBlen 16 --soloUMIstart 39
-chromiumV2_illumina:
-  filter_R1_length: 56
+  illumina:
+    filter_R1_length: 58
+    STAR_R1: --soloUMIlen 12 --clip5pNbases 58 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
+    STAR_R2: --soloUMIlen 12
+  element:
+    filter_R1_length: False
+    STAR_R1: --soloUMIlen 12 --clip5pNbases 48 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17
+    STAR_R2: --soloUMIlen 12
+  ultima:
+    filter_R1_length: 58
+    STAR_R1: --soloUMIlen 9 --clip5pNbases 58 --soloCBstart 23 --soloCBlen 16 --soloUMIstart 39
+chromiumV2:
   bc_whitelist: WHITELIST_V2
-  STAR_R1: --soloUMIlen 10 --clip5pNbases 56 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
-  STAR_R2: --soloUMIlen 10
-dropseq_illumina:
-  filter_R1_length: 50
-  STAR_R1: --soloUMIlen 8 --clip5pNbases 50 0 --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
-  STAR_R2: --soloUMIlen 8 --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13
-microwellseq_illumina:
-  filter_R1_length: 54
+  illumina:
+    filter_R1_length: 56
+    STAR_R1: --soloUMIlen 10 --clip5pNbases 56 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
+    STAR_R2: --soloUMIlen 10
+dropseq:
+  illumina:
+    filter_R1_length: 50
+    STAR_R1: --soloUMIlen 8 --clip5pNbases 50 0 --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
+    STAR_R2: --soloUMIlen 8 --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13
+microwellseq:
   bc_cut: CGACTCACTACAGGG...TCGGTGACACGATCG
-  STAR_R1: --soloUMIlen 6 --clip5pNbases 54 0 --soloCBstart 1 --soloCBlen 18 --soloUMIstart 19 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
-  STAR_R2:  --soloUMIlen 6 --soloCBstart 1 --soloCBlen 18 --soloUMIstart 19
-bd_illumina:
-  filter_R1_length: 53
+  illumina:
+    filter_R1_length: 54
+    STAR_R1: --soloUMIlen 6 --clip5pNbases 54 0 --soloCBstart 1 --soloCBlen 18 --soloUMIstart 19 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
+    STAR_R2:  --soloUMIlen 6 --soloCBstart 1 --soloCBlen 18 --soloUMIstart 19
+bd:
   bc_cut: ACTGGCCTGCGA...GGTAGCGGTGACA
-  STAR_R1: --soloUMIlen 8 --clip5pNbases 53 0 --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
-  STAR_R2: --soloUMIlen 8 --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28
-indrop_illumina:
-  filter_R1_length: 32
-  STAR_R1: --soloUMIlen 6 --clip5pNbases 32 0 --soloCBstart 1 --soloCBlen 8 --soloUMIstart 9 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
-  STAR_R2: --soloUMIlen 6 --soloCBstart 1 --soloCBlen 8 --soloUMIstart 9
-
+  illumina:
+    filter_R1_length: 53
+    STAR_R1: --soloUMIlen 8 --clip5pNbases 53 0 --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
+    STAR_R2: --soloUMIlen 8 --soloCBstart 1 --soloCBlen 27 --soloUMIstart 28
+indrop:
+  illumina:
+    filter_R1_length: 32
+    STAR_R1: --soloUMIlen 6 --clip5pNbases 32 0 --soloCBstart 1 --soloCBlen 8 --soloUMIstart 9 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2
+    STAR_R2: --soloUMIlen 6 --soloCBstart 1 --soloCBlen 8 --soloUMIstart 9
diff --git a/config.yaml b/config.yaml
@@ -35,7 +35,8 @@ POLYA_SITES:
 
 DEFAULTS:
 # default config options, overridden by SAMPLES and CHEMISTRY definitions
-  chemistry: chromiumV3_illumina
+  platform: illumina
+  chemistry: chromiumV3
   alignments:
     - R2
     - paired
@@ -53,13 +54,16 @@ SAMPLES:
 #   extra star_args (STAR_R1_extra_args, STAR_R2_extra_args, STAR_paired_extra_args)
   test:
     basename: sample
-    chemistry: chromiumV2_illumina
+    platform: illumina
+    chemistry: chromiumV2
   test2:
     basename: dropseq
-    chemistry: dropseq_illumina
+    platform: illumina
+    chemistry: dropseq
   test3:
     basename: microwellseq
-    chemistry: microwellseq_illumina
+    platform: illumina
+    chemistry: microwellseq
 
 
 # for multiqc report