fix issue #31

Snakefile

@@ -133,21 +133,20 @@ elif config["genome"]["rRNA_mapping"]:
 
 def mapping_index(wildcards):
     if (wildcards.REF == config["genome"]["name"]):
-        input = config["genome"]["fasta_file"]
+        return {"fasta": config["genome"]["fasta_file"]}
     elif (wildcards.REF == config["genome"]["host_name"]):
-        input = config["genome"]["host_fasta_file"]
+        return {"fasta": config["genome"]["host_fasta_file"]}
     elif (wildcards.REF == "Ribo" ):
-        input = config["genome"]["ribo_fasta_file"]    
-    return(input)
+        return {"fasta": config["genome"]["ribo_fasta_file"]}
     
 def annot_index(wildcards):
     if (wildcards.REF == config["genome"]["name"]):
-        input = config["genome"]["gff_file"]
+        return {"gff_file": config["genome"]["gff_file"]}
     elif (wildcards.REF == config["genome"]["host_name"]):
-        input = config["genome"]["host_gff_file"]
+        return {"gff_file": config["genome"]["host_gff_file"]}
     elif (wildcards.REF == "Ribo" ):
-        input = ""
-    return(input)
+        return {"gff_file": ""}
+
 
 
 
@@ -161,7 +160,7 @@ if config["bowtie2_mapping"]["do"]:
     mapper += ["bowtie2"]
     if config["genome"]["index"]: 
         # indexing for bowtie2
-        bowtie2_index_fasta = mapping_index
+        bowtie2_index_fasta = unpack(mapping_index)
         bowtie2_index_output_done = os.path.join(os.path.dirname(config["genome"]["fasta_file"]), "{REF}.1.bt2")
         bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"],"{REF}")
         bowtie2_index_log = "02-Mapping/bowtie2/logs/bowtie2_{REF}_indexing.log"
@@ -193,10 +192,10 @@ if config["bowtie2_mapping"]["do"]:
 if config["star_mapping"]["do"]: 
     mapper += ["STAR"]
     if config["genome"]["index"]: 
-        star_index_fasta = mapping_index
+        star_index_fasta = unpack(mapping_index)
         star_index_output_done = os.path.join(config["genome"]["genome_directory"],"{REF}/SAindex")
         star_index_output_dir = os.path.join(config["genome"]["genome_directory"],"{REF}")
-        star_mapping_splice_file = annot_index
+        star_mapping_splice_file = unpack(annot_index)
         star_index_log = "02-Mapping/STAR/logs/STAR_{REF}_indexing.log"
         include: os.path.join(RULES, "star_index.rules")
 

workflow/rules/adapters.rules

+#########################################################################
+# RNAflow: an automated pipeline to analyse transcriptomic data         #
+#                                                                       #
+# Authors: Rachel Legendre                                              #
+# Copyright (c) 2021-2022  Institut Pasteur (Paris).                    #
+#                                                                       #
+# This file is part of RNAflow workflow.                                #
+#                                                                       #
+# RNAflow is free software: you can redistribute it and/or modify       #
+# it under the terms of the GNU General Public License as published by  #
+# the Free Software Foundation, either version 3 of the License, or     #
+# (at your option) any later version.                                   #
+#                                                                       #
+# RNAflow is distributed in the hope that it will be useful,            #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the          #
+# GNU General Public License for more details .                         #
+#                                                                       #
+# You should have received a copy of the GNU General Public License     #
+# along with RNAflow (LICENSE).                                         #
+# If not, see <https://www.gnu.org/licenses/>.                          #
+#########################################################################
+
+
+
+
+rule adapters:
+    input:
+        fastq = adapters_input_fastq
+    output:
+        adapters_output
+    params:
+        wkdir = adapters_wkdir,
+        options = adapters_options,
+        adapters = adapters_adapt_list,
+        mode = adapters_mode,
+	    min = adapters_min,
+	    qual = adapters_qual
+    singularity:
+        "rnaflow.img"
+    threads: config['adapters']['threads']
+    log:
+        adapters_log
+    envmodules:
+        "cutadapt",
+        "cutadapt-devel"
+    shell:
+        """
+        set +o pipefail
+        
+    	tmp="{input}"
+            infiles=($tmp)
+    	
+    	tmp="{output}"
+    	outfiles=($tmp)	
+    
+        # add mode and adapter sequences
+        cmd+=" cutadapt -{params.mode} {params.adapters} -m {params.min} -q {params.qual} {params.options}  "
+        # paired end or single end
+        if [[ ${{#infiles[@]}} -eq 2 ]];
+        then
+            cmd+=" -o ${{outfiles[0]}} -p ${{outfiles[1]}}  ${{infiles[0]}} ${{infiles[1]}} "
+        else
+            cmd+=" -o ${{outfiles[0]}} ${{infiles[0]}}"
+        fi
+        #run command
+        eval "${{cmd}} > {log}"
+
+        """

workflow/rules/basicCoverage.rules

+#########################################################################
+# RNAflow: an automated pipeline to analyse transcriptomic data         #
+#                                                                       #
+# Authors: Rachel Legendre                                              #
+# Copyright (c) 2021-2022  Institut Pasteur (Paris).                    #
+#                                                                       #
+# This file is part of RNAflow workflow.                                #
+#                                                                       #
+# RNAflow is free software: you can redistribute it and/or modify       #
+# it under the terms of the GNU General Public License as published by  #
+# the Free Software Foundation, either version 3 of the License, or     #
+# (at your option) any later version.                                   #
+#                                                                       #
+# RNAflow is distributed in the hope that it will be useful,            #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the          #
+# GNU General Public License for more details .                         #
+#                                                                       #
+# You should have received a copy of the GNU General Public License     #
+# along with RNAflow (LICENSE).                                         #
+# If not, see <https://www.gnu.org/licenses/>.                          #
+#########################################################################
+
+
+
+rule basicCoverage:
+    input:
+        basicCoverage_input
+    log:
+        basicCoverage_logs
+    output:
+        basicCoverage_output
+    singularity:
+        "rnaflow.img"
+    params:
+        options = basicCoverage_options
+    envmodules:
+        "samtools",
+        "bedtools"
+    shell:
+        """
+        
+        samtools view -f 0x10 -b {input} | bedtools genomecov -ibam stdin -bg > $rev
+        samtools view -F 0x10 -b {input} | bedtools genomecov -ibam stdin -bg > $fwd
+        bamCoverage --bam {input} --outFileName {output} {params.options}  2> {log}
+        """
+
+

workflow/rules/bowtie2_index.rules

@@ -26,7 +26,7 @@
 
 rule bowtie2_index:
     input:
-        fasta =  bowtie2_index_fasta
+        bowtie2_index_fasta
     output:
         bowtie2_index_output_done
     singularity:
@@ -40,7 +40,10 @@ rule bowtie2_index:
         "samtools"
     shell:
         """
-        bowtie2-build {input.fasta} {params.prefix}  2> {log}
-        samtools faidx {input.fasta} 2>> {log}
+        set +o pipefail
+
+        #compute index
+        bowtie2-build {input} {params.prefix}  2> {log}
+        samtools faidx {input} 2>> {log}
 
         """

workflow/rules/star_index.rules

@@ -25,12 +25,12 @@
 
 rule star_index:
     input:
-       fasta =  star_index_fasta
+        star_index_fasta,
+        star_mapping_splice_file
     output:
         star_index_output_done
     params:
-        wkdir = star_index_output_dir,
-        splice_file = star_mapping_splice_file
+        wkdir = star_index_output_dir
     singularity:
         "rnaflow.img"
     log:
@@ -42,16 +42,17 @@ rule star_index:
         "samtools"
     shell:
         """
-        GenomeLength=`grep -v ">" {star_index_fasta} | tr -d '\n' | wc -c`
-        SAindex=$(echo $GenomeLength | awk '{{a=log($1)/2 - 1; if (a>14) a=14; printf("%d\n",a)}}')
+        set +o pipefail
+        GenomeLength=`grep -v ">" {input} | tr -d '\n' | wc -c`
+        SAindex=$(echo $GenomeLength | awk '{{a=log($1)/2 - 1; if (a>14) a=14; printf("%d\\n",a)}}')
         
         
-        if [[ -s {params.splice_file} && {params.splice_file} == "*.gtf"  ]]
+        if [[ -s {input.gff_file} && {input.gff_file} == "*.gtf"  ]]
         then
-            STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile {params.splice_file} --genomeSAindexNbases $SAindex
-        elif [[ -s {params.splice_file} && {params.splice_file} == "*.gff" ]]
+            STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile {input.gff_file} --genomeSAindexNbases $SAindex
+        elif [[ -s {input.gff_file} && {input.gff_file} == "*.gff" ]]
         then
-             STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile {params.splice_file} --sjdbGTFtagExonParentTranscript Parent --genomeSAindexNbases $SAindex
+             STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile {input.gff_file} --sjdbGTFtagExonParentTranscript Parent --genomeSAindexNbases $SAindex
         else
             STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --genomeSAindexNbases $SAindex
         fi