Merge pull request #10 from ruppinlab/feat-Robinson2023

Feat Robinson2023

Author: wir963

.gitignore

@@ -1,3 +1,4 @@
+data/*
 **/.snakemake
 **/.DS_Store
 **/output

Ben-Moshe2019/run-SRPRISM.smk

@@ -41,7 +41,7 @@ rule add_CR_tags_SRPRISM:
         SRPRISM_CB_UMI_TABLE,
         SRPRISM_CB_UMI_COUNT
     script:
-        "src/add_CR_tags_to_SRPRISM_bam.py"
+        "../src/add_CR_tags_to_SRPRISM_bam.py"
 
 # get a read count per gene per sample file
 rule intersect_BAM_GFF:

Lee2020/Snakefile

@@ -0,0 +1,85 @@
+from os.path import join
+import pandas as pd
+from snakemake.utils import min_version
+##### set minimum snakemake version #####
+min_version("5.1.2")
+
+##### load config and sample sheets #####
+configfile: "config/PathSeq-config.yaml"
+
+
+
+cells = pd.read_csv(config["units"], sep="\t").set_index(["sample", "barcode", "patient"], drop=False)
+
+samples = pd.read_csv(config["samples"], sep="\t").set_index(["patient", "sample"], drop=False)
+# samples = samples.loc[samples["Maximum read length"] == "57bp"]
+cells = cells.loc[cells["sample"].isin(samples["sample"])]
+# samples = cells[["patient", "sample", "library_id", "sample_prefix"]].reset_index(drop=True).drop_duplicates().set_index(["patient", "sample"], drop=False)
+# samples = samples.iloc[0:2]
+
+# cells = cells.loc[cells.patient.isin(["H08", "H37"])]
+wildcard_constraints:
+    patient="|".join(samples["patient"]),
+    sample="|".join(samples["sample"])
+
+# Snakemake includes
+# include: "../RNA-snakemake-rules/rules/cellranger.smk"
+include: "../pathogen-discovery-rules/rules/PathSeq-10x.smk"
+
+# Directories
+CR_SAMPLE_ODIR = "{patient}-{sample}"
+FASTQ_DIR = "/data/Robinson-SB/scRNAseq_46samples_fastq/{library}"
+
+# CellRanger Files
+CR_BAM_FILE = join(CR_SAMPLE_ODIR, "outs", "possorted_genome_bam.bam")
+
+PATIENT_FASTQ_DIR = join("FASTQ", "raw", "{patient}")
+
+# cellranger complains when you pass directory as --id
+CR_SAMPLE_ODIR = "{patient}-{sample}"
+
+
+
+
+# PathSeq files
+PATHSEQ_BAM = join("output", "PathSeq", "{patient}-{sample}", "pathseq.bam")
+PATHSEQ_CELL_SCORE = join("output", "PathSeq", "{patient}-{sample}-{cell}", "pathseq.txt")
+
+rule all:
+    input:
+        # expand(PATHSEQ_BAM, zip, patient=samples["patient"], sample=samples["sample"]),
+        expand(PATHSEQ_CELL_SCORE, zip, patient=cells["patient"], sample=cells["sample"], cell=cells["barcode"])
+        #expand(SRPRISM_TAG_BAM, zip, patient=samples["patient"], sample=samples["sample"], genome=samples["genome"])
+
+def get_cellranger_input_directory(wildcards):
+    library_id = samples.loc[(wildcards.patient, wildcards.sample), "library_id"]
+    return {
+        "dir": expand(FASTQ_DIR, library=library_id)
+    }
+
+def get_library_id(wildcards):
+    return samples.loc[(wildcards.patient, wildcards.sample), "sample_prefix"]
+
+# expected input format for FASTQ file
+rule cellranger_count:
+    input:
+        unpack(get_cellranger_input_directory)
+    params:
+        PATIENT_FASTQ_DIR,
+        CR_SAMPLE_ODIR,
+        config["CellRanger"]["genome_dir"],
+        config["CellRanger"]["chemistry"],
+        get_library_id
+    output:
+        CR_BAM_FILE
+    shell:
+        "module load cellranger/5.0.1 && "
+        # snakemake auto creates directories for output files but cellranger expects existing directories to pipestance directory
+        "rm -rf {params[1]} && "
+        "cellranger count --id={params[1]} "
+        "--fastqs={input[0]}/ " # this is the path to the directory containing the FASTQ files
+        "--sample={params[4]} " # this is the sample to use
+        "--transcriptome={params[2]} "
+        "--localcores=$SLURM_CPUS_PER_TASK "
+        "--chemistry={params[3]} "
+        "--localmem=60"

Lee2020/data/patients.tsv

@@ -3,9 +3,6 @@ patients: data/patients.tsv
 samples: data/samples.tsv
 units: data/units.tsv
 
-trimming:
-  skip: True
-
 PathSeq:
   bam_file: "output/BAM/{patient}-{sample}-unaligned.bam"
   microbe_fasta: "../data/microbev1.fa"
@@ -20,7 +17,7 @@ VecScreen:
   contaminant_hits: "../data/microbev1-vecscreen-combined-matches.bed"
 
 params:
-  PathSeq: "--min-clipped-read-length 50 --min-base-quality 1 --max-masked-bases 10 --dust-t 24 "
+  PathSeq: "--min-clipped-read-length 38 --min-base-quality 1 --max-masked-bases 10 --dust-t 24"
   PathSeqScore: ""
 
 CellRanger:

Lee2020/data/samples.tsv

@@ -35,6 +35,11 @@
       "mem": "150g",
       "time": "4:00:00"
     },
+    "add_CR_tags_SRPRISM":
+    {
+      "mem": "150g",
+      "time": "4:00:00"
+    },
     "split_PathSeq_BAM_by_CB_UB":
     {
       "mem": "8g",
@@ -45,6 +50,11 @@
     {
       "mem": "32g",
       "time": "4:00:00",
-      "nthreads": 16
+      "nthreads": 1 
+    },
+    "run_CAMMiQ_species_long_reads":
+    {
+      "mem": "650g",
+      "partition": "largemem"
     }
 }

Lee2020/data/units.tsv

@@ -0,0 +1,47 @@
+patient	sample	S_ID	library_id	sample_prefix	Maximum read length	10x_chemistry	cancer_type
+C25	C25	S038	9_XW_SC_1-26-2017	9_XW_SC_1-26-2017	57bp	v2	CCA
+C26	C26a	S020	Sample_CS023169_Wang_0823_1626-12-23_SCAF350	CS023169_Wang_0823_1626-12-23_SCAF350	98bp	v2	CCA
+C26	C26b	S037	8_XW_SC_1-26-2017	8_XW_SC_1-26-2017	57bp	v2	CCA
+C29	C29	S040	11_XW_SC_3-1-2017	11_XW_SC_3-1-2017	57bp	v2	CCA
+C35	C35	S045	20_XW_SC_7-26-2017	20_XW_SC_7-26-2017	57bp	v2	CCA
+C39	C39	S044	19_XW_SC_7-27-2017	19_XW_SC_7-27-2017	57bp	v2	CCA
+C42	C42	S025	Sample_CS023169_Wang_0823_1642_SCAF355	CS023169_Wang_0823_1642_SCAF355	98bp	v2	CCA
+C46	C46a	S027	Sample_CS023169_Wang_0823_1646-12-1_SCAF357	CS023169_Wang_0823_1646-12-1_SCAF357	98bp	v2	CCA
+C46	C46b	S028	Sample_CS023169_Wang_0824_1646-1-17_SCAF358	CS023169_Wang_0824_1646-1-17_SCAF358	98bp	v2	CCA
+C52	C52	S016	Sample_CS023169_Wang_0731_1652_SCAF303	CS023169_Wang_0731_1652_SCAF303	98bp	v2	CCA
+C56	C56	S018	Sample_CS023169_Wang_0731_1656_SCAF305	CS023169_Wang_0731_1656_SCAF305	98bp	v2	CCA
+C60	C60	S015	Sample_CS023169_Wang_0730_1660r_SCAF300	CS023169_Wang_0730_1660r_SCAF300	98bp	v2	CCA
+C66	C66	S034	Sample_CS023169_Wang_0824_1666_SCAF365	CS023169_Wang_0824_1666_SCAF365	98bp	v2	CCA
+C76	C76	S010	CS025253_SCAF880_LCS1676	CS025253_SCAF880_LCS1676	98bp	v2	CCA
+H08	H08	S001	CS024371_SCAF529_LCS1608	CS024371_SCAF529_LCS1608	98bp	v2	HCC
+H18	H18	S043	16_XW_SC_6-13-2017	16_XW_SC_6-13-2017	57bp	v2	HCC
+H21	H21	S035	2_XW_SC_10-25-2016	2_XW_SC_10-25-2016	57bp	v2	HCC
+H23	H23	S039	10_XW_SC_2-2-2017	10_XW_SC_2-2-2017	57bp	v2	HCC
+H28	H28	S036	7_XW_SC_1-12-2017	7_XW_SC_1-12-2017	57bp	v2	HCC
+H30	H30	S041	12_XW_SC_3-2-2017	12_XW_SC_3-2-2017	57bp	v2	HCC
+H34	H34b	S021	Sample_CS023169_Wang_0823_1634-1-10_SCAF352	CS023169_Wang_0823_1634-1-10_SCAF352	98bp	v2	HCC
+H34	H34a	S022	Sample_CS023169_Wang_0823_1634-12-1_SCAF351	CS023169_Wang_0823_1634-12-1_SCAF351	98bp	v2	HCC
+H34	H34c	S023	Sample_CS023169_Wang_0823_1634-4-15_SCAF353	CS023169_Wang_0823_1634-4-15_SCAF353	98bp	v2	HCC
+H37	H37	S046	21_XW_SC_8-1-2017	21_XW_SC_8-1-2017	57bp	v2	HCC
+H38	H38	S042	15_XW_SC_6-8-2017	15_XW_SC_6-8-2017	57bp	v2	HCC
+H41	H41	S024	Sample_CS023169_Wang_0823_1641_SCAF354	CS023169_Wang_0823_1641_SCAF354	98bp	v2	HCC
+H43	H43	S026	Sample_CS023169_Wang_0823_1643_SCAF356	CS023169_Wang_0823_1643_SCAF356	98bp	v2	HCC
+H49	H49b	S008	CS025253_SCAF872_LCS1649	CS025253_SCAF872_LCS1649	98bp	v2	HCC
+H49	H49a	S029	Sample_CS023169_Wang_0824_1649_SCAF359	CS023169_Wang_0824_1649_SCAF359	98bp	v2	HCC
+H54	H54	S014	Sample_CS023169_Wang_0730_1654_SCAF301	CS023169_Wang_0730_1654_SCAF301	98bp	v2	HCC
+H55	H55	S017	Sample_CS023169_Wang_0731_1655_SCAF304	CS023169_Wang_0731_1655_SCAF304	98bp	v2	HCC
+H58	H58c	S012	SCAF637	SCAF637	98bp	v2	HCC
+H58	H58a	S030	Sample_CS023169_Wang_0824_1658-5-31_SCAF361	CS023169_Wang_0824_1658-5-31_SCAF361	98bp	v2	HCC
+H58	H58b	S031	Sample_CS023169_Wang_0824_1658-7-11_SCAF362	CS023169_Wang_0824_1658-7-11_SCAF362	98bp	v2	HCC
+H62	H62	S019	Sample_CS023169_Wang_0731_1662r_SCAF307	CS023169_Wang_0731_1662r_SCAF307	98bp	v2	HCC
+H63	H63	S032	Sample_CS023169_Wang_0824_1663_SCAF363	CS023169_Wang_0824_1663_SCAF363	98bp	v2	HCC
+H65	H65	S033	Sample_CS023169_Wang_0824_1665_SCAF364	CS023169_Wang_0824_1665_SCAF364	98bp	v2	HCC
+H68	H68a	S011	SCAF372	SCAF372	98bp	v2	HCC
+H68	H68b	S013	SCAF589	SCAF589	98bp	v2	HCC
+H70	H70	S002	CS023169_SCAF592	CS023169_SCAF592	98bp	v2	HCC
+H72	H72	S003	CS023169_SCAF672	CS023169_SCAF672	98bp	v3	HCC
+H73	H73a	S004	CS023169_SCAF694	CS023169_SCAF694	98bp	v3	HCC
+H73	H73b	S006	CS025253_SCAF765_LCS1673_2	CS025253_SCAF765_LCS1673_2	98bp	v2	HCC
+H74	H74	S005	CS025253_SCAF764_LCS1674	CS025253_SCAF764_LCS1674	98bp	v2	HCC
+H75	H75	S007	CS025253_SCAF850_LCS1675	CS025253_SCAF850_LCS1675	98bp	v2	HCC
+H77	H77	S009	CS025253_SCAF873_LCS1677	CS025253_SCAF873_LCS1677	98bp	v2	HCC