fix issue #32

Snakefile

@@ -99,7 +99,7 @@ include: os.path.join(RULES, "fastqc.rules")
 if config["adapters"]["remove"] :
 
     ## TODO add AlienTrimmer
-    adapter_tool = "adapters"
+    adapter_tool = "cutadapt"
     adapters_input_fastq = input_data
     adapters_wkdir = "01-Trimming"
     adapters_output = ["01-Trimming/{SAMPLE}_R1_trim.fastq.gz"]
@@ -114,7 +114,7 @@ if config["adapters"]["remove"] :
     adapters_qual = config["adapters"]["quality"]
     adapters_log = "01-Trimming/logs/{SAMPLE}_trim.txt"
     final_output.extend(expand(adapters_output, SAMPLE=samples))
-    include: os.path.join(RULES, "adapters.rules")
+    include: os.path.join(RULES, "cutadapt.rules")
 
 else:
     adapters_output = input_data
@@ -206,6 +206,7 @@ if config["star_mapping"]["do"]:
         
     #first pass mapping
     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_output_prefix =  "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_init_"
@@ -217,6 +218,7 @@ if config["star_mapping"]["do"]:
     
     #Second pass mapping
     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_output_prefix =  "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_"

config/config.yaml

@@ -55,7 +55,7 @@ tmpdir: "/pasteur/sonic/scratch/public/"
 
 genome:
     index: true
-    genome_directory: /path/to/genome/
+    #genome_directory: /path/to/genome/
     name: saccer3
     fasta_file: /path/to/genome/saccer3.fa
     gff_file: /path/to/genome/saccer3.gff

workflow/rules/alienTrimmer.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:
+        "AlienTrimmer/2.0"
+    shell:
+        """
+        set +o pipefail
+        
+    	tmp="{input}"
+        infiles=($tmp)
+    	
+    	tmp="{output}"
+    	outfiles=($tmp)	
+    
+        # add mode and adapter sequences
+        cmd+="AlienTrimmer -c {params.adapters} -l {params.min} -q {params.qual} {params.options} -z"
+        # paired end or single end
+        if [[ ${{#infiles[@]}} -eq 2 ]];
+        then
+            cmd+=" -o ${{outfiles[0]}} -p ${{outfiles[1]}} -1 ${{infiles[0]}} -2 ${{infiles[1]}} "
+        else
+            cmd+=" -o ${{outfiles[0]}} -i ${{infiles[0]}}"
+        fi
+        #run command
+        eval "${{cmd}} > {log}"
+
+        """

workflow/rules/kallisto_index.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 kallisto_index:
+    input:
+       fasta =  kallisto_index_fasta
+    output:
+        kallisto_index_output
+    params:
+        kmer = kallisto_index_kmer
+    singularity:
+        "rnaflow.img"
+    log:
+        kallisto_index_log
+    threads:
+        config['kallisto']['threads']
+    envmodules:
+        "kallisto/0.46.2"
+    shell:
+        """
+        
+        kallisto index -i {output} --kmer-size={params.kmer}   {input.fasta}
+
+        """ 

workflow/rules/kallisto_quant.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 kallisto_quant:
+    input:
+       index = kallisto_quant_index,
+       fastq = kallisto_quant_fastq
+    output:
+        directory(kallisto_quant_output_dir)
+    params:
+        options = kallisto_quant_options
+    singularity:
+        "rnaflow.img"
+    log:
+        kallisto_pseudo_log
+    threads:
+        config['kallisto']['threads']
+    envmodules:
+        "kallisto/0.46.2"
+    shell:
+        """
+       
+        kallisto quant -t {threads} {params.options} -o {output} -i {input.index} {input.fastq}
+
+        """ 

workflow/rules/star_mapping_pass1.rules

@@ -25,11 +25,12 @@
 rule star_mapping_pass1:
     input:
         fastq = star_mapping_pass1_input,
-        index = star_mapping_pass1_index
+        done = star_mapping_pass1_done
     output:
         jontion = temp(star_mapping_pass1_junctions),
         bam = temp(star_mapping_pass1_bam)
     params:
+        index = star_mapping_pass1_index,
         prefix = temp(star_mapping_pass1_output_prefix),
         #read_groups = star_mapping_pass1_read_groups,
         kwargs = config['star_mapping']['options']
@@ -44,7 +45,7 @@ rule star_mapping_pass1:
         star_mapping_pass1_logs
     shell:
         """ 
-        STAR --genomeDir {input.index} \
+        STAR --genomeDir {params.index} \
              --readFilesIn {input.fastq}  \
              --runThreadN {threads} \
              --genomeLoad NoSharedMemory \

workflow/rules/star_mapping_pass2.rules

@@ -25,12 +25,13 @@
 rule star_mapping_pass2:
     input:
         fastq = star_mapping_pass2_input,
-        index = star_mapping_pass2_index,
+        done = star_mapping_pass2_done,
         sjdb = star_mapping_pass2_junctions,
         bam = star_mapping_pass2_bam
     output:
         star_mapping_pass2_sort
     params:
+        index = star_mapping_pass2_index,
         prefix = temp(star_mapping_pass2_output_prefix),
         RG = star_mapping_pass2_read_groups,
         kwargs = config['star_mapping']['options']
@@ -45,7 +46,7 @@ rule star_mapping_pass2:
         star_mapping_pass2_logs
     shell:
         """ 
-        STAR --genomeDir {input.index} \
+        STAR --genomeDir {params.index} \
              --readFilesIn {input.fastq}  \
              --runThreadN {threads} \
              --genomeLoad NoSharedMemory \