Support for single-end data

MINTIE_SE.groovy

@@ -0,0 +1,310 @@
+/*
+  __  __ ___ _   _ _____ ___ _____
+ |  \/  |_ _| \ | |_   _|_ _| ____|
+ | |\/| || ||  \| | | |  | ||  _|
+ | |  | || || |\  | | |  | || |___
+ |_|  |_|___|_| \_| |_| |___|_____|
+
+Method for Inferring Novel Transcripts and Isoforms using Equivalences classes
+
+Author: Marek Cmero
+*/
+
+code_base = file(bpipe.Config.config.script).parentFile.absolutePath
+load code_base + "/tools.groovy"
+load code_base + "/references.groovy"
+
+// initialise defaults if not provided
+if(!binding.variables.containsKey("fastqCaseFormat")){
+    fastqCaseFormat="cases/%_R*.fastq.gz"
+}
+if(!binding.variables.containsKey("fastqControlFormat")){
+    fastqControlFormat="controls/%_R*.fastq.gz"
+}
+if(!binding.variables.containsKey("assemblyFasta")){
+    assemblyFasta=""
+}
+if(!binding.variables.containsKey("run_de_step")){
+    run_de_step="true"
+}
+if(!binding.variables.containsKey("splice_motif_mismatch")){
+    splice_motif_mismatch=0
+}
+
+fastq_dedupe = {
+    from("*.gz"){
+        def sample_name = branch.name
+        output.dir = sample_name
+        produce(sample_name+'.1.fastq.gz'){
+            exec """
+            $dedupe $input.gz $output
+            """, "fastq_dedupe"
+        }
+    }
+}
+
+trim = {
+    output.dir = branch.name
+    produce('trim1.fastq.gz') {
+        if (assemblyFasta != '') {
+            // no need to trim if assembly provided
+            exec """
+            touch $output1 ; touch $output2
+            """
+        } else {
+            exec """
+            $trimmomatic SE -threads $threads -phred$scores $input1
+                $output1.prefix
+                LEADING:$minQScore TRAILING:$minQScore MINLEN:$min_read_length ;
+            gzip $output1.prefix  ;
+            """, "trim"
+        }
+    }
+}
+
+assemble = {
+    def sample_name = branch.name
+    def Ks_for_soap = Ks.toString().contains(',') ? Ks.split(',').join(' ') : Ks
+    output.dir = sample_name
+    produce(sample_name + '_denovo_filt.fasta'){
+        if (assemblyFasta != '') {
+            exec """
+            ln -s $assemblyFasta $output ;
+            """
+        } else if (assembler.toLowerCase() == 'trinity') {
+            exec """
+            $Trinity --seqType fq --max_memory ${assembly_mem}G --output $sample_name/trinity_assembly \
+                --left $input1 --right $input2 --CPU $threads ;
+            ln -s trinity_assembly/Trinity.fasta $output ;
+            """, "assemble"
+        } else if (assembler.toLowerCase() == 'spades') {
+            exec """
+            $rnaspades -1 $input1 -2 $input2 -k $Ks -t $threads -m $assembly_mem -o $sample_name/SPAdes_assembly ;
+            ln -s SPAdes_assembly/contigs.fasta $output ;
+            """, "assemble"
+        } else {
+            exec """
+            rlens=`gunzip -c $input1 \
+                       | awk -v mrl=$min_read_length 'BEGIN {minlen = mrl; maxlen = 0} {
+                            if (NR % 4 == 2) {
+                                rlen = length(\$1) ;
+                                if (rlen > maxlen) {maxlen = rlen}
+                                if (rlen < minlen) {minlen = rlen}
+                            }} END {print minlen" "maxlen}'` ;
+            min_rlen=\${rlens% *} ;
+            max_rlen=\${rlens#* } ;
+
+            if [ ! -d $output.dir/SOAPassembly ]; then
+                mkdir $output.dir/SOAPassembly ;
+            fi ;
+            cd $output.dir/SOAPassembly ;
+
+            echo \"max_rd_len=\$max_rlen\" > config.config ;
+            echo -e \"[LIB]\\nq=../../$input1\" >> config.config ;
+            if [ -e SOAP.fasta ]; then rm SOAP.fasta ; fi ;
+            for k in $Ks_for_soap ; do
+                if [ \$k -gt \$min_rlen ]; then
+                    echo "WARNING: Kmer size \$k exceeds minimum read length \${min_rlen}. Please double check parameters." ;
+                else
+                    $soapdenovotrans pregraph -s config.config -o outputGraph_\$k -K \$k -p $threads ;
+                    $soapdenovotrans contig -g outputGraph_\$k ;
+                    cat outputGraph_\$k.contig | sed "s/^>/>k\${k}_/g" >> SOAP.fasta ;
+                fi ;
+            done ;
+
+            cd ../../ ;
+            $dedupe in=$sample_name/SOAPassembly/SOAP.fasta out=stdout.fa threads=$threads overwrite=true | \
+                $fasta_formatter | \
+                awk '!/^>/ { next } { getline seq } length(seq) > $min_contig_len { print \$0 "\\n" seq }' > $output ;
+            if [ ! -s $output ] ; then
+                rm $output ;
+                echo "ERROR: de novo assembled contigs fasta file is empty." ;
+                echo "Please check paths for SOAPdenovoTrans, dedupe and fasta" ;
+                echo "formatter are correct, and their dependencies are installed." ;
+            fi ;
+            """, "assemble"
+        }
+    }
+}
+
+create_salmon_index = {
+    def sample_name = branch.name
+    def salmon_index = sample_name + "/all_fasta_index"
+    output.dir = salmon_index
+    def index_fasta = output.dir + "/" + sample_name + ".fasta"
+    produce(index_fasta, '*.bin'){
+        exec """
+        cat $trans_fasta $input.fasta > $output1 ;
+        $salmon index -t $output1 -i $salmon_index -p $threads ;
+        """, "create_salmon_index"
+    }
+}
+
+run_salmon = {
+    def workingDir = System.getProperty("user.dir");
+    def rf = inputs.split().collect { workingDir+"/$it" }[0]
+    def salmon_index="all_fasta_index"
+    def base_outdir = "salmon_out"
+    def controls_dir = fastqControlFormat.split("/")[-2]
+    def sample_name = branch.name
+
+    if(type == "controls"){
+        sample_name = branch.parent.parent.name
+        def control_name = branch.name
+
+        output.dir = sample_name + "/" + controls_dir + "/" + control_name + "_salmon_out/aux_info"
+        base_outdir = control_name + "_salmon_out"
+        salmon_index = "../all_fasta_index"
+    } else {
+        output.dir = sample_name + "/salmon_out/aux_info"
+    }
+
+    produce("eq_classes.txt*"){
+        exec """
+        cd $output.dir/../.. ;
+        $salmon quant --dumpEq --seqBias --validateMappings --hardFilter -i $salmon_index -l A -r $rf -p $threads -o $base_outdir
+        """, "run_salmon"
+    }
+}
+
+create_ec_count_matrix = {
+    def sample_name = branch.name
+    def sample_names = inputs.split().collect { it.split('/')[-3].split('_salmon_out')[0] }
+    sample_names.set(0, sample_name) // case sample, rest are controls
+    sample_names = sample_names.join(',')
+    output.dir = sample_name
+    produce("ec_count_matrix.txt"){
+        exec """
+        $python $code_base/DE/create_ec_count_matrix.py $inputs $sample_names $output1 ;
+        """, "create_ec_count_matrix"
+    }
+}
+
+run_de = {
+    def run_de_bool = run_de_step.toBoolean()
+    def sample_name = branch.name
+    output.dir = sample_name
+    produce("eq_classes_de.txt"){
+        if(run_de_bool) {
+            exec """
+            ${R}script $code_base/DE/compare_eq_classes.R $sample_name $input $trans_fasta $output --FDR=$fdr --minCPM=$min_cpm --minLogFC=$min_logfc
+            """, "run_de"
+        } else {
+            exec """
+            $python $code_base/DE/get_novel_contigs.py $input $trans_fasta $output.dir/${sample_name}_denovo_filt.fasta
+            """, "run_de"
+        }
+    }
+}
+
+filter_on_significant_ecs = {
+    def sample_name = branch.name
+    output.dir = sample_name
+    produce("de_contigs.fasta"){
+        exec """
+        $python $code_base/util/filter_fasta.py $output.dir/${sample_name}_denovo_filt.fasta $input.txt --col_id contig > $output1 ;
+        """, "filter_sig_ecs"
+    }
+}
+
+align_contigs_against_genome = {
+    def sample_name = branch.name
+    output.dir = sample_name
+    produce('aligned_contigs_against_genome.sam'){
+        exec """
+        $gmap -D $gmap_refdir -d $gmap_genome -f samse -t $threads -x $min_gap --max-intronlength-ends=500000 -n 0 $input.fasta > $output
+        """, "align_contigs_against_genome"
+    }
+}
+
+annotate_contigs = {
+    def sample_name = branch.name
+    output.dir = sample_name
+    produce("annotated_contigs.vcf", "annotated_contigs_info.tsv", "annotated_contigs.bam"){
+        exec """
+        $python ${code_base}/annotate/annotate_contigs.py \
+            $sample_name $input.bam \
+            $ann_info $tx_annotation \
+            $output.bam $output.tsv \
+            --minClip $min_clip \
+            --minGap $min_gap \
+            --minMatch $min_match \
+            --log $output.dir/annotate.log > $output.vcf
+        """, "annotate_contigs"
+    }
+}
+
+refine_contigs = {
+    def sample_name = branch.name
+    output.dir = sample_name
+    produce("novel_contigs.vcf", "novel_contigs_info.tsv", "novel_contigs.bam", "novel_contigs.fasta"){
+        exec """
+        $python ${code_base}/annotate/refine_annotations.py \
+            $input.tsv $input.vcf $input.bam $tx_annotation \
+            $genome_fasta $output.prefix \
+            --minClip $min_clip \
+            --minGap $min_gap \
+            --mismatches $splice_motif_mismatch \
+            --log $output.dir/refine.log > $output.vcf ;
+        $samtools index $output.bam ;
+        $python $code_base/util/filter_fasta.py $input.fasta $output.tsv --col_id contig_id > $output.fasta ;
+        """, "refine_contigs"
+    }
+}
+
+calculate_VAF = {
+    output.dir = branch.name
+    produce("vaf_estimates.txt"){
+        exec """
+        ${R}script ${code_base}/annotate/estimate_VAF.R $branch.name/ec_count_matrix.txt $branch.name/salmon_out/quant.sf $input.tsv $trans_fasta $tx2gene $output
+        """, "calculate_VAF"
+    }
+}
+
+post_process = {
+    def sample_name = branch.name
+    def var_filter = var_filter.split(',').join(' ')
+    def gf_arg = gene_filter == '' ? '' : '--gene_filter ' + gene_filter
+    def vf_arg = var_filter == '' ? '' : '--var_filter ' + var_filter
+    output.dir = sample_name
+    produce(sample_name + '_results.tsv'){
+        exec """
+        $python ${code_base}/annotate/post_process.py \
+            $sample_name \
+            $input.tsv \
+            $input.fasta \
+            $sample_name/eq_classes_de.txt \
+            $sample_name/vaf_estimates.txt \
+            $gf_arg \
+            $vf_arg \
+            --log $output.dir/postprocess.log > $output
+        """
+    }
+}
+
+sort_and_index_bam = {
+    output.dir = new File(input.sam).getParentFile()
+    transform('sam') to ('bam') {
+        exec """
+        $samtools sort -@ $threads -m ${sort_ram} $input.sam -o $output ;
+        $samtools index $output
+        """, "sort_and_index_bam"
+    }
+}
+
+run { fastqCaseFormat * [ fastq_dedupe +
+                          trim +
+                          assemble +
+                          create_salmon_index +
+                          [ fastqCaseFormat * [ run_salmon.using(type: "case") ],
+                            fastqControlFormat * [ run_salmon.using(type:"controls") ] ] +
+                          create_ec_count_matrix +
+                          run_de +
+                          filter_on_significant_ecs +
+                          align_contigs_against_genome +
+                          sort_and_index_bam +
+                          annotate_contigs +
+                          refine_contigs +
+                          calculate_VAF +
+                          post_process ]
+}

mintie

@@ -26,7 +26,8 @@ do
         echo -e "\nusage (setup references): mintie -r "
         echo -e "\nusage (setup test data): mintie -t "
         echo -e "\nusage (wrapper): mintie -w -p [params.txt] cases/*.fastq.gz controls/*.fastq.gz "
-        echo -e "\nusage (direct):\n export \$MINTIEDIR=$MINTIE_HOME;\n bpipe run -@$MINTIEDIR/params.txt  [ <other bpipe options >] \n\t \$MINTIEDIR/MINTIE.groovy cases/*.fastq.gz controls/*fastq.gz"
+        echo -e "\nusage (direct):\n export \$MINTIEDIR=$MINTIE_HOME;\n bpipe run -@\$MINTIEDIR/params.txt  [ <other bpipe options >] \n\t \$MINTIEDIR/MINTIE.groovy cases/*.fastq.gz controls/*fastq.gz"
+        echo -e "\nusage (direct single-end):\n export \$MINTIEDIR=$MINTIE_HOME;\n bpipe run -@\$MINTIEDIR/params.txt  [ <other bpipe options >] \n\t \$MINTIEDIR/MINTIE_SE.groovy cases/*.fastq.gz controls/*fastq.gz"
         echo ""
         exit 0
         shift

test/run_test_se.sh

@@ -0,0 +1,13 @@
+#!/bin/sh
+
+# modify reference to control fasta
+grep -v allvars-control references.groovy > backup_references.groovy
+echo "trans_fasta=\"$PWD/test/data/allvars-control.fasta\"" > tmp.txt
+cat backup_references.groovy tmp.txt > references.groovy ; rm tmp.txt
+
+cases=`ls test/data/cases/*gz | grep R1`
+controls=`ls test/data/controls/*gz | grep R1`
+bpipe @test/test_params.txt MINTIE_SE.groovy $cases $controls
+
+# restore original references
+mv backup_references.groovy references.groovy