fix: replace 3' specific cutadapt rules with a specific cutadapt setu…

…p in the config.yaml for the 3' test

.test/3-prime-config/config/config.yaml

@@ -120,8 +120,11 @@ params:
   # the reverse reads of paired end sequencing:
   # * https://cutadapt.readthedocs.io/en/stable/guide.html#trimming-paired-end-reads
   cutadapt-se:
-    adapters: "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
-    extra: "-q 20"
+    # This setup is for Lexogen QuantSeq FWD data, based on (but simplfied):
+    # https://faqs.lexogen.com/faq/what-is-the-adapter-sequence-i-need-to-use-for-t-1
+    # For more details, see the QuantSeq section in the `config/README.md` file.
+    adapters: "-a r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=7;max_error_rate=0.005"
+    extra: "--minimum-length 33 --nextseq-trim=20 --poly-a"
   # reasoning behind parameters:
   #   For reads that are produced by 3’-end sequencing, depending on the protocol, it might be recommended to remove some leading bases (e.g. see https://www.nature.com/articles/s41598-019-55434-x#Sec10)
   #   * `--minimum-length 33`:
@@ -134,5 +137,5 @@ params:
   #   * `--minimum-overlap 7`: the cutadapt default minimum overlap of `5` did trimming on the level
   #     of expected adapter matches by chance
   cutadapt-pe: 
-    adapters: "-a ACGGATCGATCGATCGATCGAT -g GGATCGATCGATCGATCGAT -A ACGGATCGATCGATCGATCGAT -G GGATCGATCGATCGATCGAT"
-    extra: "--minimum-length 33 -e 0.005 --overlap 7"
+    adapters: ""
+    extra: ""

workflow/rules/trim.smk

@@ -15,19 +15,29 @@ rule cutadapt_pe:
         "v1.22.0/bio/cutadapt/pe"
 
 
-if not is_3prime_experiment:
+rule cutadapt:
+    input:
+        get_fastqs,
+    output:
+        fastq="results/trimmed/{sample}-{unit}.fastq.gz",
+        qc="results/trimmed/{sample}-{unit}.qc.txt",
+    threads: 8
+    params:
+        adapters=config["params"]["cutadapt-se"]["adapters"],
+        extra=config["params"]["cutadapt-se"]["extra"],
+    log:
+        "results/logs/cutadapt/{sample}-{unit}.log",
+    wrapper:
+        "v1.22.0/bio/cutadapt/se"
 
-    rule cutadapt:
-        input:
-            get_fastqs,
-        output:
-            fastq="results/trimmed/{sample}-{unit}.fastq.gz",
-            qc="results/trimmed/{sample}-{unit}.qc.txt",
-        threads: 8
-        params:
-            adapters=config["params"]["cutadapt-se"]["adapters"],
-            extra=config["params"]["cutadapt-se"]["extra"],
-        log:
-            "results/logs/cutadapt/{sample}-{unit}.log",
-        wrapper:
-            "v1.22.0/bio/cutadapt/se"
+rule max_read_length:
+    input:
+        get_all_fastqs,
+    output:
+        "results/stats/max-read-length.json",
+    log:
+        "logs/max-read-length.log",
+    conda:
+        "../envs/pysam.yaml"
+    script:
+        "../scripts/get-max-read-length.py"