Merge branch 'main' of github.com:boulardlab/3t-seq

workflow/Snakefile

@@ -36,7 +36,7 @@ include: "rules/common.smk"
 ###########################
 
 
-containerized: "docker://ftabaro/rna-seq:1.2"
+containerized: "docker://ftabaro/rna-seq:1.3"
 
 
 #######################
@@ -133,6 +133,7 @@ init_folders = [
     tables_folder,
     pictures_folder,
     notebooks_folder,
+    fastqc_raw_folder,
 ]
 
 

workflow/rules/common.smk

@@ -159,17 +159,18 @@ def get_fastq_paired(wildcards):
 
 
 def get_fastq(wildcards):
-    if wildcards.serie in library_names_single:
-        for p in raw_reads_folder.joinpath(wildcards.serie).iterdir():
-            gd = parse_filepath(p)
-            if gd["sample"] == wildcards.sample:
-                return p
-        raise ValueError(
-            "Could not determine input files for serie: {}".format(wildcards.serie)
+    for p in raw_reads_folder.joinpath(wildcards.serie).iterdir():
+        gd = parse_filepath(p)
+        s = gd["sample"]
+        if gd["mate"] != "":
+            s += gd["mate"]
+        if s == wildcards.sample:
+            return p
+    raise ValueError(
+        "Could not determine input files for serie: {}\nsample: {}\n{}".format(
+            wildcards.serie, wildcards.sample, gd
         )
-    else:
-        ret = list(get_fastq_paired(wildcards).values())
-        return ret
+    )
 
 
 def mkdir(p: Path, verbose=False):