Trimmomatic single-end

assnake_core_preprocessing/trimmomatic/workflow.smk

@@ -1,18 +1,34 @@
+from assnake.core.dataset import Dataset
+import os
+
+def inputs(wildcards):
+    if Dataset(wildcards.df).dataset_type == 'paired-end':
+        return [
+                wc_config['fastq_gz_R1_wc'],
+                wc_config['fastq_gz_R2_wc'],
+                os.path.join(config['assnake_db'], "presets/trimmomatic/{preset}.json"),
+                ]
+    else:
+        return [
+                wc_config['fastq_gz_R1_wc'],
+                os.path.join(config['assnake_db'], "presets/trimmomatic/{preset}.json"),
+                ]
+
 rule tmtic:
-    input:
-        first=wc_config['fastq_gz_R1_wc'],
-        second=wc_config['fastq_gz_R2_wc'],
-        params=os.path.join(config['assnake_db'], "presets/trimmomatic/{preset}.json")
-    output:
-        r1=wc_config['fastq_gz_tmtic_R1_wc'],
+    input: inputs
+    output: 
+        r1=wc_config['fastq_gz_tmtic_R1_wc']
+    params: 
         r2=wc_config['fastq_gz_tmtic_R2_wc'],
-        u =wc_config['fastq_gz_tmtic_S_wc']
-    params:
+        u =wc_config['fastq_gz_tmtic_S_wc'],
         u1=wc_config['fastq_gz_tmtic_unpaired1_wc'],
-        u2=wc_config['fastq_gz_tmtic_unpaired2_wc']
+        u2=wc_config['fastq_gz_tmtic_unpaired2_wc'],
+        dataset_type=lambda wildcards: Dataset(wildcards.df).dataset_type
+
     log: "{fs_prefix}/{df}/reads/{preproc}__tmtic_{preset}/{df_sample}.log"
     threads: 8#config['assnake-core-preprocessing']['results']['trimmomatic']['threads']
     wildcard_constraints:    
         params="[\w\d_-]+",
     conda: 'env_0.38.yaml'
-    wrapper: "file://"+os.path.join(config['assnake-core-preprocessing']['install_dir'], 'trimmomatic/wrapper.py')
+    wrapper: "file://"+os.path.join(config['assnake-core-preprocessing']['install_dir'], 'trimmomatic/wrapper.py')
+

assnake_core_preprocessing/trimmomatic/wrapper.py

@@ -1,6 +1,7 @@
 from snakemake.shell import shell
 import json, os
 
+
 def tmtic_params(params_loc):
     params_str = ''
     params_dict = {}
@@ -45,18 +46,28 @@ def tmtic_params(params_loc):
 
     return params_str
 
-param_str = tmtic_params(snakemake.input.params)
-
-shell('''echo "start installing tmmtic"
-        trimmomatic PE -phred33 \
+param_str = tmtic_params(snakemake.input[-1])
+
+if snakemake.params.dataset_type == 'paired-end':        
+    shell('''echo "start installing tmmtic"
+            trimmomatic PE -phred33 \
+                     -threads {snakemake.threads} \
+                     {snakemake.input[0]} {snakemake.input[1]} \
+                     {snakemake.output.r1} {snakemake.params.u1} \
+                     {snakemake.params.r2} {snakemake.params.u2} \
+                     {param_str} \
+             >{snakemake.log} 2>&1 && \
+             cat {snakemake.params.u1} {snakemake.params.u2} | gzip > {snakemake.params.u} 2>>{snakemake.log} && \
+             rm {snakemake.params.u1} {snakemake.params.u2} 2>>{snakemake.log}''')
+else:
+    shell('''echo "start installing tmmtic"
+        trimmomatic SE -phred33 \
                  -threads {snakemake.threads} \
-                 {snakemake.input.first} {snakemake.input.second} \
-                 {snakemake.output.r1} {snakemake.params.u1} \
-                 {snakemake.output.r2} {snakemake.params.u2} \
+                 {snakemake.input[0]} \
+                 {snakemake.output.r1} \
                  {param_str} \
          >{snakemake.log} 2>&1 && \
-         cat {snakemake.params.u1} {snakemake.params.u2} | gzip > {snakemake.output.u} 2>>{snakemake.log} && \
-         rm {snakemake.params.u1} {snakemake.params.u2} 2>>{snakemake.log}''')
+         2>>{snakemake.log}''')
 
 if 'task_id' in snakemake.config.keys():
     save_to_db(config['task_id'], 'tmtic', str(input), str(log), 'RUN SUCCESSFUL')