added cutadapt -m=1 to snakefiles to avoid empty reads, updated doc

pipeline_documentation.md

@@ -557,7 +557,7 @@ Remove adapter sequences from reads with
     - Adapters to be removed; specify in sample table columns `fq1_3p`, `fq1_5p`,
     `fq2_3p`, `fq2_5p`
   - **rule_config.yaml:**
-    - `-m 10`: Discard processed reads that are shorter than 10 (default 0, that might cause problems in downstream programs)
+    - `-m 10`: Discard processed reads that are shorter than 10 (default 0; Because empty reads will cause problems in downstream programs, -m=1 is hardcoded in the snakefile. That value will be overwritten by the value specified in `rule_config.yaml`)
     - `-n 2`: search for all the given adapter sequences repeatedly, either until
     no adapter match was found or until 2 rounds have been performed. (default 1)
 
@@ -579,7 +579,7 @@ Remove poly(A) tails from reads with
   - **samples.tsv**
     - Poly(A) stretches to be removed; specify in sample table columns `fq1_polya` and `fq2_polya`
   - **rule_config.yaml**
-      - `-m 10`: Discard processed reads that are shorter than 10 (default 0, that might cause problems in downstream programs)
+    - `-m 10`: Discard processed reads that are shorter than 10 (default 0; Because empty reads will cause problems in downstream programs, -m=1 is hardcoded in the snakefile. That value will be overwritten by the value specified in `rule_config.yaml`)
       - `-O 1`: minimal overlap of 1 (default: 3)
 - **Output**
   - Reads file (`.fastq.gz`); used in

tests/input_files/rule_config.yaml

@@ -96,23 +96,27 @@ prepare_bigWig:
 remove_adapters_cutadapt:
     # search for all the given adapter sequences repeatedly, either until no adapter match was found or until n rounds have been performed. (default 1, ZARP recommends 2)
     -n: '2'
-    # Discard processed reads that are shorter than 10 (default 0, ZARP strongly recommends m > 0, because empty reads might cause problems in downstream programs)
+    # Discard processed reads that are shorter than m (default 0, ZARP strongly recommends m > 0, because empty reads will cause problems in downstream programs; 
+    # Hardcoded to -m=1 in both snakefiles; that value will be overwritten by the -m value specified here!)
     -m: '10'
 
 pe_remove_adapters_cutadapt:
     # search for all the given adapter sequences repeatedly, either until no adapter match was found or until n rounds have been performed. (default 1, ZARP recommends 2)
     -n: '2'
-    # Discard processed reads that are shorter than 10 (default 0, ZARP strongly recommends m > 0, because empty reads might cause problems in downstream programs)
+    # Discard processed reads that are shorter than m (default 0, ZARP strongly recommends m > 0, because empty reads will cause problems in downstream programs; 
+    # Hardcoded to -m=1 in both snakefiles; that value will be overwritten by the -m value specified here!)
     -m: '10'
 
 remove_polya_cutadapt:
-    # Discard processed reads that are shorter than 10 (default 0, ZARP strongly recommends m > 0, because empty reads might cause problems in downstream programs)
+    # Discard processed reads that are shorter than m (default 0, ZARP strongly recommends m > 0, because empty reads will cause problems in downstream programs; 
+    # Hardcoded to -m=1 in both snakefiles; that value will be overwritten by the -m value specified here!)
     -m: '10'
     # Minimal overlap of adapter and read (default 3, ZARP recommends 1 in order to remove all 3' As)
     -O: '1' 
 
 pe_remove_polya_cutadapt:
-    # Discard processed reads that are shorter than 10 (default 0, ZARP strongly recommends m > 0, because empty reads might cause problems in downstream programs)
+    # Discard processed reads that are shorter than m (default 0, ZARP strongly recommends m > 0, because empty reads will cause problems in downstream programs; 
+    # Hardcoded to -m=1 in both snakefiles; that value will be overwritten by the -m value specified here!)
     -m: '10'
     # Minimal overlap of adapter and read (default 3, ZARP recommends 1 in order to remove all 3' As)
     -O: '1' 

workflow/rules/paired_end.snakefile.smk

@@ -79,6 +79,7 @@ rule pe_remove_adapters_cutadapt:
         -g {params.adapter_5_mate1} \
         -A {params.adapter_3_mate2} \
         -G {params.adapter_5_mate2} \
+        -m 1 \
         {params.additional_params} \
         -o {output.reads1} \
         -p {output.reads2} \
@@ -177,6 +178,7 @@ rule pe_remove_polya_cutadapt:
         -g {params.polya_5_mate1} \
         -A {params.polya_3_mate2} \
         -G {params.polya_5_mate2} \
+        -m 1 \
         {params.additional_params} \
         -o {output.reads1} \
         -p {output.reads2} \

workflow/rules/single_end.snakefile.smk

@@ -66,6 +66,7 @@ rule remove_adapters_cutadapt:
         -j {threads} \
         -a {params.adapters_3} \
         -g {params.adapters_5} \
+        -m 1 \
         {params.additional_params} \
         -o {output.reads} \
         {input.reads}) \
@@ -140,6 +141,7 @@ rule remove_polya_cutadapt:
         -j {threads} \
         -a {params.polya_3} \
         -g {params.polya_5} \
+        -m 1 \
         {params.additional_params} \
         -o {output.reads} \
         {input.reads};) \