nextseq fix merged to IMP3anna

workflow/rules/Preprocessing/trimming.smk

@@ -11,8 +11,6 @@ if config['nextseq']:
             'Preprocessing/{type}.se2.trimmoed.fq'
         threads: 10
         params:
-            adapter = lambda wildcards: config["trimmomatic"]["adapter"][wildcards.type]
-        resources:
             runtime="12:00:00",
             mem = MEMCORE
         conda: ENVDIR + "/IMP_preprocessing.yaml"
@@ -21,7 +19,7 @@ if config['nextseq']:
         shell:
             """
             trimmomatic PE -threads {threads} {input[0]} {input[1]} {output} \
-             ILLUMINACLIP:{DBPATH}/adapters/{params.adapter}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
+             ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
              LEADING:{config[trimmomatic][leading]} \
              TRAILING:{config[trimmomatic][trailing]} \
              SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \
@@ -38,7 +36,7 @@ if config['nextseq']:
         wildcard_constraints:
             read="se[1|2]"
         threads: 10
-        resources:
+        params:
             runtime="12:00:00",
             mem = MEMCORE
         conda: ENVDIR + "/IMP_preprocessing.yaml"
@@ -58,11 +56,14 @@ if config['nextseq']:
         output:
             'Preprocessing/{type}.r1.trimmed.fq',
             'Preprocessing/{type}.r2.trimmed.fq',
-            'Preprocessing/{type}.seCut.trimmed.fq',
+            'Preprocessing/{type}.r1Cut.trimmed.fq',
+            'Preprocessing/{type}.r2Cut.trimmed.fq',
+            'Preprocessing/{type}.se1Cut.trimmed.fq',
+            'Preprocessing/{type}.se2Cut.trimmed.fq',
             'Preprocessing/{type}.r1.trimmoed.fq.gz',
             'Preprocessing/{type}.r2.trimmoed.fq.gz'
         threads: 10
-        resources:
+        params:
             runtime="12:00:00",
             mem = MEMCORE
         conda: ENVDIR + "/IMP_preprocessing.yaml"
@@ -72,24 +73,36 @@ if config['nextseq']:
             """
             cutadapt -j {threads} --nextseq-trim={config[trimmomatic][trailing]} \
              --minimum-length {config[trimmomatic][minlen]}:{config[trimmomatic][minlen]} \
-             -o {output[0]} -p {output[1]} --too-short-paired-output {output[2]} {input[0]} {input[1]} >> {log} 2>&1
+             -o {output[0]} -p {output[1]} --too-short-output {output[2]} --too-short-paired-output {output[3]} \
+             {input[0]} {input[1]} >> {log} 2>&1
+            cutadapt -j {threads} \
+             --minimum-length {config[trimmomatic][minlen]} \
+             -o {output[4]} {output[2]} >> {log} 2>&1
+            cutadapt -j {threads} \
+             --minimum-length {config[trimmomatic][minlen]} \
+             -o {output[5]} {output[3]} >> {log} 2>&1
             pigz -p {threads} {input} >> {log} 2>&1
             """
     rule cat_se_trimmed:
         input:
             'Preprocessing/{type}.se1.trimmed.fq',
             'Preprocessing/{type}.se2.trimmed.fq',
-            'Preprocessing/{type}.seCut.trimmed.fq'
+            'Preprocessing/{type}.se1Cut.trimmed.fq',
+            'Preprocessing/{type}.se2Cut.trimmed.fq',
+            'Preprocessing/{type}.r1Cut.trimmed.fq',
+            'Preprocessing/{type}.r2Cut.trimmed.fq'
         output:
-            'Preprocessing/{type}.se.trimmed.fq'
+            'Preprocessing/{type}.se.trimmed.fq',
         threads: 1
-        resources:
+        params:
             runtime="12:00:00",
             mem = MEMCORE
+        conda: ENVDIR + "/IMP_preprocessing.yaml"
         message: "cat_se_trimmed: Concatenating trimmed single end {wildcards.type} reads"
         shell:
             """
-            cat {input[0]} {input[1]} > {output}
+            cat {input[0]} {input[1]} {input[2]} {input[3]} > {output}
+            pigz -p {threads} {input}
             """
 else:
     rule trimming:
@@ -104,8 +117,6 @@ else:
             'Preprocessing/{type}.se2.trimmed.fq'
         threads: 10
         params:
-            adapter = lambda wildcards: config["trimmomatic"]["adapter"][wildcards.type]
-        resources:
             runtime="12:00:00",
             mem = MEMCORE
         conda: ENVDIR + "/IMP_preprocessing.yaml"
@@ -114,7 +125,7 @@ else:
         shell:
             """
             trimmomatic PE -threads {threads} {input[0]} {input[1]} {output} \
-             ILLUMINACLIP:{DBPATH}/adapters/{params.adapter}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
+             ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
              LEADING:{config[trimmomatic][leading]} \
              TRAILING:{config[trimmomatic][trailing]} \
              SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \
@@ -129,7 +140,7 @@ else:
         output:
             'Preprocessing/{type}.se.trimmed.fq'
         threads: 1
-        resources:
+        params:
             runtime="12:00:00",
             mem = MEMCORE
         message: "cat_se_trimmed: Concatenating trimmed single end {wildcards.type} reads"