Merge branch 'main' into include_dsb

CHANGELOG.md

@@ -1,10 +1,13 @@
 # Changelog
 
-## [1.0.5] - 2024-01-XX
+## [1.0.6] - 2024-11-XX
 
 ### Added
 - include as default `dsb` ambient protein background correction for ADT counts, for experiments without hashing deconvolution
 
+## [1.0.5] - 2024-10-09 
+- removed `SeqRunName` variable, as it is not needed by cellranger anymore
+
 ## [1.0.4] - 2023-09-19
 
 ### Changed

config/README.md

@@ -29,22 +29,15 @@ A pre-configured samplemap ready to run on the test data that can be adapted is
 Example samplemap:
 
 ```
-sample    HashingFile     SeqRunName      nTargetCells    featureReferenceFile
-sampleA   HashingFileA    SeqRunNameA     10000           featureReferenceFileA
-sampleB   HashingFileB    SeqRunNameB     15000           featureReferenceFileB
+sample    HashingFile     nTargetCells    featureReferenceFile
+sampleA   HashingFileA    10000           featureReferenceFileA
+sampleB   HashingFileB    15000           featureReferenceFileB
 ```
 
 With one line per set of samples
 
 - `sample` contains the sample identifier that is used throughout the pipeline
 - `HashingFile` contains the full path to the comma separated text file containing the hashtag barcodes and their assignment to individual sample names (see [HashingFile](#hashingfile)).
-- `SeqRunName` corresponds to the sequencing sample name of the ADT sample; this parameter is only required for the Cellranger run of ADT data. It can be retrieved from the FASTQ file names as follows:
-
-```
-[SeqRunName]_S[Number]_L00[Lane Number]_[Read Type]_001.fastq.gz
-```
-
-Where Read Type is one of: I1, R1, R2.
 
 - `nTargetCells` corresponds to the number of targeted cells for the sample.
 - `featureReferenceFile` corresponds to the ADT feature reference file for the sample set. For further information please consult the Cellranger tool documentation.  

config/samplemap

@@ -1,2 +1,2 @@
-sample	HashingFile	SeqRunName	nTargetCells	featureReferenceFile
-PBMC_D1	testdata/HashingFile_PBMC_D1.csv	BSSE_QGF_132646_HHVFNDRXX_1_PBMC_mix_20k_ADT_E3_SI-NA-E3	20000	testdata/feature_reference.txt
+sample	HashingFile	nTargetCells	featureReferenceFile
+PBMC_D1	testdata/HashingFile_PBMC_D1.csv	20000	testdata/feature_reference.txt

workflow/rules/adt_cellranger.smk

@@ -17,7 +17,6 @@ rule create_library_file_adt:
         library_file=WORKDIR
         + "/results/pooled_samples/cellranger_adt/{sample_set}.adt_library.txt",
     params:
-        seqRunName=getSeqRunName,
     threads: config["computingResources"]["threads"]["low"]
     resources:
         mem_mb=config["computingResources"]["mem_mb"]["low"],

workflow/rules/misc_snake.smk

@@ -120,17 +120,6 @@ def getTargetCellsCellranger_simple(wildcards):
     return out
 
 
-# Retrieve the ADT sequencing run name corresponding to a given sample set
-def getSeqRunName(wildcards):
-    # Create dictionary with samples and SeqRunName
-    sampleMap = dict(zip(samples["sample"], samples["SeqRunName"]))
-    if wildcards.sample_set not in sampleMap.keys():
-        raise ValueError(
-            "Sample '%s' not found in the sample map!" % (wildcards.sample_set)
-        )
-    return sampleMap[wildcards.sample_set]
-
-
 # Retrieve the ADT feature reference file corresponding to a given sample set
 def getFeatRefFile(wildcards):
     # Create dictionary with samples and FeatureRefFile

workflow/schema/sample_map.schema.yaml

@@ -7,9 +7,6 @@ properties:
   HashingFile:
     type: string
     description: Path to the Tag File
-  SeqRunName:
-    type: string
-    description: Sequencing sample name of ADT Fastq Files
   nTargetCells:
     type: integer
     description: The number of cells that were targeted in the lab
@@ -20,7 +17,6 @@ properties:
 required:
   - sample
   - HashingFile
-  - SeqRunName
   - nTargetCells
   - featureReferenceFile