allow rule trim_adapters to use all CPUs available

rules/preprocess.smk

@@ -30,24 +30,24 @@ BBMAP_REF_DIR = config['preprocess']['bbmap_ref_dir']
 # It provides a report with quality check, before and after processing
 rule trim_adapters:
     input:
-        fwd=lambda wildcards: ['{}/{}/{}-R1.fastq.gz'.format(RAW_FASTQ_DIR, DATASETSX[ix], value)
+        fwd = lambda wildcards: ['{}/{}/{}-R1.fastq.gz'.format(RAW_FASTQ_DIR, DATASETSX[ix], value)
         for ix,value in enumerate(FASTQS) if value==wildcards.fastq_file],
         #RAW_FASTQ_DIR+'/{dataset}/{fastq_file}-R1.fastq.gz',
-        rev=lambda wildcards: ['{}/{}/{}-R2.fastq.gz'.format(RAW_FASTQ_DIR, DATASETSX[ix], value)
+        rev = lambda wildcards: ['{}/{}/{}-R2.fastq.gz'.format(RAW_FASTQ_DIR, DATASETSX[ix], value)
         for ix,value in enumerate(FASTQS) if value==wildcards.fastq_file],
         #RAW_FASTQ_DIR+'/{dataset}/{fastq_file}-R2.fastq.gz'
     output:
-        fwd_tr=temp(PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}-R1.fastp.fastq.gz'),
-        rev_tr=temp(PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}-R2.fastp.fastq.gz'),
-        report1=PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}.fastp.html',
-        report2=PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}.fastp.json'
+        fwd_tr = temp(PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}-R1.fastp.fastq.gz'),
+        rev_tr = temp(PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}-R2.fastp.fastq.gz'),
+        report1 = PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}.fastp.html',
+        report2 = PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}.fastp.json'
     log:
         LOGS_DIR + '/preprocess/{dataset}_atrimmed/{fastq_file}.log'
     params:
-        fastp_dir=PRE_PROC_DIR,
+        fastp_dir = PRE_PROC_DIR,
         adapter = config['preprocess']['adapter'],
         min_length = config['preprocess']['min_length']
-    threads: int(cpus_avail/4)
+    threads: cpus_avail
     singularity: singularity_img
     group: 'preprocess'
     shell:
@@ -71,9 +71,9 @@ rule trim_adapters:
 #
 rule filter_human:
     input:
-        human_ref=BBMAP_REF_DIR,
-        fwd_tr=rules.trim_adapters.output.fwd_tr,
-        rev_tr=rules.trim_adapters.output.rev_tr
+        human_ref = BBMAP_REF_DIR,
+        fwd_tr = rules.trim_adapters.output.fwd_tr,
+        rev_tr = rules.trim_adapters.output.rev_tr
         #fwd_tr=PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}-R1.fastp.fastq.gz',
         #rev_tr=PRE_PROC_DIR+'/{dataset}_atrimmed/{fastq_file}-R2.fastp.fastq.gz'
     output:
@@ -174,13 +174,13 @@ rule trim3end_dedupe:
         fwd_clean_dedup = PRE_PROC_DIR+'/{dataset}_cdedupe/{fastq_file}-R1.clean.nodup.fastq.gz',
         rev_clean_dedup = PRE_PROC_DIR+'/{dataset}_cdedupe/{fastq_file}-R2.clean.nodup.fastq.gz'
     params:
-        fastp_dir=PRE_PROC_DIR,
+        fastp_dir = PRE_PROC_DIR,
         min_length = config['preprocess']['min_length']
     output:
-        fwd_tr=PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}-R1.clean.nodup.fastp.fastq.gz',
-        rev_tr=PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}-R2.clean.nodup.fastp.fastq.gz',
-        report1=PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}.clean.nodup.fastp.html',
-        report2=PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}.clean.nodup.fastp.json'
+        fwd_tr = PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}-R1.clean.nodup.fastp.fastq.gz',
+        rev_tr = PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}-R2.clean.nodup.fastp.fastq.gz',
+        report1 = PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}.clean.nodup.fastp.html',
+        report2 = PRE_PROC_DIR+'/{dataset}_dfinaltrim/{fastq_file}.clean.nodup.fastp.json'
     threads: int(cpus_avail/4)
     singularity: singularity_img
     group: 'preprocess'
@@ -199,10 +199,12 @@ rule trim3end_dedupe:
 rule multiqc_preprocess_listing_files:
     input:
         #
-        atrimmed=lambda wildcards: ['{}/{}_atrimmed/{}.fastp.json'.format(PRE_PROC_DIR, value, FASTQS[ix])
+        atrimmed = lambda wildcards: ['{}/{}_atrimmed/{}.fastp.json'.format(
+        PRE_PROC_DIR, value, FASTQS[ix])
         for ix,value in enumerate(DATASETSX) if value==wildcards.dataset],
         #
-        dfinaltrim=lambda wildcards: ['{}/{}_dfinaltrim/{}.clean.nodup.fastp.json'.format(PRE_PROC_DIR, value, FASTQS[ix])
+        dfinaltrim = lambda wildcards: ['{}/{}_dfinaltrim/{}.clean.nodup.fastp.json'.format(
+        PRE_PROC_DIR, value, FASTQS[ix])
         for ix,value in enumerate(DATASETSX) if value==wildcards.dataset]
     output:
         multiqc_input_list = PRE_PROC_REPORT+'/{dataset}_multiqc_inputs.txt'
@@ -221,7 +223,7 @@ rule multiqc_preprocess:
     input:
         PRE_PROC_REPORT+'/{dataset}_multiqc_inputs.txt'
     output:
-        multiqc_report=report(PRE_PROC_REPORT+'/{dataset}_multiqc.html',
+        multiqc_report = report(PRE_PROC_REPORT+'/{dataset}_multiqc.html',
         category='preprocess')
     singularity: singularity_img
     shell: