gestion of gz

Snakefile

@@ -181,7 +181,7 @@ if config["bowtie2_mapping"]["do"]:
 
     # indexing for bowtie2
     bowtie2_index_fasta = unpack(mapping_index)
-    bowtie2_index_log = "02-Mapping/bowtie2/logs/bowtie2_{REF}_indexing.log"
+    bowtie2_index_log = "02-Mapping/{REF}/bowtie2/logs/bowtie2_{REF}_indexing.log"
     bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2")
     bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}")
                    
@@ -211,7 +211,7 @@ if config["star_mapping"]["do"]:
     mapper += ["STAR"]
     star_index_fasta = unpack(mapping_index)
     star_mapping_splice_file = unpack(annot_index)
-    star_index_log = "02-Mapping/STAR/logs/STAR_{REF}_indexing.log"
+    star_index_log = "02-Mapping/{REF}/STAR/logs/STAR_{REF}_indexing.log"
     star_index_output_done = config["genome"]["genome_directory"]+"/{REF}/STAR/SAindex"
     star_index_output_dir = config["genome"]["genome_directory"]+"/{REF}/STAR/" 
  
@@ -222,7 +222,7 @@ if config["star_mapping"]["do"]:
     star_mapping_pass1_input = adapters_output
     star_mapping_pass1_done = star_index_output_done
     star_mapping_pass1_index = star_index_output_dir
-    star_mapping_pass1_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}_init.out"
+    star_mapping_pass1_logs = "02-Mapping/{REF}/STAR//logs/{SAMPLE}_{REF}_init.out"
     star_mapping_pass1_output_prefix =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_"
     star_mapping_pass1_junctions = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_SJ.out.tab"
     star_mapping_pass1_bam =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_Aligned.sortedByCoord.out.bam"
@@ -234,7 +234,7 @@ if config["star_mapping"]["do"]:
     star_mapping_pass2_input = adapters_output
     star_mapping_pass2_done = star_index_output_done
     star_mapping_pass2_index = star_index_output_dir
-    star_mapping_pass2_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}.out"
+    star_mapping_pass2_logs = "02-Mapping/{REF}/STAR//logs/{SAMPLE}_{REF}.out"
     star_mapping_pass2_output_prefix =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_"
     star_mapping_pass2_junctions = expand("02-Mapping/{{REF}}/STAR/{SAMPLE}_{{REF}}_init_SJ.out.tab", SAMPLE=samples)
     star_mapping_pass2_bam = star_mapping_pass1_bam

workflow/rules/alienTrimmer.rules

@@ -28,14 +28,14 @@ rule alienTrimmer:
     input:
         fastq = adapters_input_fastq
     output:
-        adapters_output
+        temp(adapters_output)
     params:
         wkdir = adapters_wkdir,
         options = adapters_options,
         adapters = config['adapters']['alien_file'],
         mode = adapters_mode,
-	    min = adapters_min,
-	    qual = adapters_qual
+        min = adapters_min,
+        qual = adapters_qual
     singularity:
         "rnaflow.img"
     shadow: "shallow"
@@ -48,11 +48,11 @@ rule alienTrimmer:
         """
         set +o pipefail
 
-    	tmp="{input}"
+        tmp="{input}"
         infiles=($tmp)
-    	
-    	tmp="{output}"
-    	outfiles=($tmp)	
+        
+        tmp="{output}"
+        outfiles=($tmp) 
     
         # add options and adapter sequences
         cmd+="AlienTrimmer -a {params.adapters} -l {params.min} -q {params.qual} {params.options}"

workflow/rules/sortmerna.rules

@@ -28,21 +28,20 @@ rule sortmerna:
         fastq = sortmerna_input,
         fasta = sortmerna_fasta
     output:
-        rRNA = sortmerna_outfile_rRNA,
-        no_rRNA = sortmerna_outfile_no_rRNA
+        rRNA = temp(sortmerna_outfile_rRNA),
+        no_rRNA = temp(sortmerna_outfile_no_rRNA)
     singularity:
         "rnaflow.img"
     log:
         err = sortmerna_logs_err,
         out = sortmerna_logs_out
-    shadow: "shallow"
     threads: 6
     envmodules:
         "sortmerna/2.1b"
     shell:
         """
         set +o pipefail
-	    #tmp="{input.fastq}"
+        #tmp="{input.fastq}"
         #infiles=($tmp)
         fasta="{input.fasta}"
         index=${{fasta%.fa}}
@@ -53,11 +52,7 @@ rule sortmerna:
         fi
 
 
-        sortmerna --ref ${{fasta}},${{index}} -a {threads} --reads {input.fastq} --aligned outfile_rRNA --fastx  --sam --num_alignments 1 --other outfile_noRNA --log -v > {log.out} 2> {log.err}
-
-
-        pigz -fc outfile_rRNA > {output.rRNA}
-        pigz -fc outfile_noRNA {output.no_rRNA}
+        sortmerna --ref ${{fasta}},${{index}} -a {threads} --reads {input.fastq} --aligned {output.rRNA} --fastx  --sam --num_alignments 1 --other {output.no_rRNA} --log -v > {log.out} 2> {log.err}
 
 
         """