Fixes for Config.yaml and Snakefile

Snakefile

@@ -62,7 +62,7 @@ def get_model_details(mtype, name):
             inputs.append(cb_txt)
         if "lr-bc" in model_dict:
             lr_matches_tsv = f"{preproc_d}/scTagger/{sample}/{sample}.lr_matches.tsv.gz"
-            params_build.append(f"--lr-bc {lr_matches_tsv}")
+            params_build.append(f"--lr-br {lr_matches_tsv}")
             inputs.append(lr_matches_tsv)
         # Outputs / Run params
         params_run.append(f"-a {Xpr_tsv}")
@@ -82,7 +82,7 @@ def get_model_details(mtype, name):
     elif mtype == "Seq":
         # Inputs / Build params
         assert set(model_dict.keys()) <= {"sample", "params"}
-        paf = get_sample_paf(sample, "badread.cDNA")
+        paf = get_badread_paf(sample, "badread.cDNA")
         params_build.append(f"--alignment {paf}")
         inputs.append(paf)
         fastqs = get_sample_fastqs(sample)
@@ -172,6 +172,9 @@ def get_sample_ref(sample, ref_type):
 def get_sample_paf(sample, ref_type):
     return f"{preproc_d}/minimap2/{sample}.{ref_type}.paf"
 
+def get_badread_paf(sample, ref_type):
+    return f"{preproc_d}/minimap2/{sample}.{ref_type}.paf.gz"
+
 
 def get_barcode_whitelist(name):
     return config["refs"]["barcodes"][name]
@@ -541,9 +544,9 @@ rule model_sequence:
     params:
         model=lambda wc: models["Seq", wc.model_name].params_build,
     shell:
-        "badread qscore_model {params.model} > {output.error_model}"
+        "badread error_model {params.model} > {output.error_model}"
         " && "
-        "badread error_model {params.model} > {output.qscore_model}"
+        "badread qscore_model {params.model} > {output.qscore_model}" 
 
 
 ### Preprocessing rules ###
@@ -611,16 +614,15 @@ rule minimap_cdna_for_badread_models:
         reads=lambda wc: get_sample_fastqs(wc.sample),
         ref=lambda wc: get_sample_ref(wc.sample, "cDNA"),
     output:
-        paf=f"{preproc_d}/badread/{{sample}}.badread.cDNA.paf",
+        paf=f"{preproc_d}/minimap2/{{sample}}.badread.cDNA.paf.gz",
     threads: 32
     shell:
         "minimap2"
         " -t {threads}"
         " -x map-ont"
         " -c"
-        " -o {output.paf}"
         " {input.ref}"
-        " {input.reads}"
+        " {input.reads} | gzip > {output.paf}"
 
 
 rule cat_refs:
@@ -636,4 +638,4 @@ rule cat_refs:
             if ref.endswith(".gz"):
                 shell("zcat {ref} >> {output.ref}")
             else:
-                shell("cat {ref} >> {output.ref}")
+                shell("cat {ref} >> {output.ref}")

config.yaml

@@ -38,7 +38,7 @@ TS_experiments:
                 params: ""
                 model: "N1"
             - plA:
-                params: ""
+                params: "--normal=15,7.5"
     head_2:
         pipeline:
             - Tsb:
@@ -48,7 +48,7 @@ TS_experiments:
                 params: ""
                 model: "N1"
             - plA:
-                params: ""
+                params: "--normal=15,7.5"
             - SCB:
                 params: ""
             - Tag:
@@ -65,7 +65,7 @@ TS_experiments:
             - Flp:
                 params: "-p 0.5"
             - Seq:
-                params: "--skip-qual-compute --badread-model nanopore2020"
+                params: "--skip-qual-compute --badread-error-model nanopore2023"
 
 exec:
     tksm: build/bin/tksm
@@ -81,6 +81,7 @@ refs:
         GTF: data/refs/Homo_sapiens.GRCh38.108.chr21.gtf
     barcodes:
         10x: data/refs/3M-february-2018.txt.gz
+    10x: data/refs/3M-february-2018.txt.gz
 
 samples:
     "MCF7-sgnex":
@@ -104,4 +105,4 @@ models:
         N1_cb-gen:
             sample: N1
             cb-txt: 10x
-            params: "--cb-count 500"
+            params: "--cb-count 500"