diff --git a/Rules/CAPmirseq-plus.snakefile b/Rules/CAPmirseq-plus.snakefile index 4871c1a..d175e8e 100644 --- a/Rules/CAPmirseq-plus.snakefile +++ b/Rules/CAPmirseq-plus.snakefile @@ -1,3 +1,22 @@ +import os + +configfile: "run.json" +abc="a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z".split(",") +BS=20 + +samples=sorted(list(config['project']['units'].keys())) +n=int(len(samples)/BS) +if len(samples)%BS !=0: + n=n+1 +batches=abc[0:n] + + +pairs=sorted(list(config['project']['pairs'].keys())) + +pfamily=config['project']['pfamily'] + + + import os configfile: "run.json" @@ -7,10 +26,10 @@ configfile: "run.json" #samples=list(config['units'].values()) #samples=[i[0].split('.fastq')[0] for i in l] -SAMPLES=":".join(config['project']['contrasts']['rsamps']) -GROUPS=":".join(config['project']['contrasts']['rgroups']) +SAMPLES=":".join(config['project']['groups']['rsamps']) +GROUPS=":".join(config['project']['groups']['rgroups']) PAIRS=":".join(config['project']['contrasts']['rcontrasts']) -samples=config['project']['contrasts']['rsamps'] +samples=config['project']['groups']['rsamps'] rule mirseq_final: input: expand("{out}/init.done",out=config['project']['workpath']), @@ -21,14 +40,14 @@ rule mirseq_final: expand("{out}/bams/{x}.bam",x=samples,out=config['project']['workpath']), expand("{out}/mirdeep2/{x}/{x}.reads.fa",x=samples,out=config['project']['workpath']), expand("{out}/mirdeep2/{x}/mirdeep2.log",x=samples,out=config['project']['workpath']), - config['project']['workpath']+"/variants/mirna_variants.vcf", - expand("{p}/qc/other_rna/{x}.gencode.genecount.txt",x=samples,p=config['project']['workpath']), +## config['project']['workpath']+"/variants/mirna_variants.vcf", +## expand("{p}/qc/other_rna/{x}.gencode.genecount.txt",x=samples,p=config['project']['workpath']), config['project']['workpath']+"/expression/mature_miRNA_expression.xls", config['project']['workpath']+"/differential_expression/expression_boxplots.pdf", config['project']['workpath']+"/SampleSummary.xls", config['project']['workpath']+"/MainDocument.html", - expand("{out}/mirspring/{x}.html",x=samples,out=config['project']['workpath']), - expand("{out}/mirspring/{x}_bwa.html",x=samples,out=config['project']['workpath']), +## expand("{out}/mirspring/{x}.html",x=samples,out=config['project']['workpath']), +## expand("{out}/mirspring/{x}_bwa.html",x=samples,out=config['project']['workpath']), rule mirseq_init: input: @@ -69,7 +88,8 @@ rule mirseq_cutadapt: params: cpath=config['bin'][pfamily]['tool_paths']['CUTADAPT_PATH'],cparams=config['bin'][pfamily]['tool_parameters']['CUTADAPT_PARAMS'],qtrim='20',indir=config['project']['workpath'],out=config['project']['workpath']+"/fastqs",mem="32G",time="4:00:00",partition="ccr",rname="mir:cutadapt" threads: 1 shell: """ - {params.cpath}/cutadapt {params.cparams} -q {params.qtrim} {input} -o {output[0]} --too-short-output={output[1]} > {output[2]} + module load cutadapt + cutadapt {params.cparams} -q {params.qtrim} {input} -o {output[0]} --too-short-output={output[1]} > {output[2]} """ rule mirseq_fastqc_pretrim: @@ -79,7 +99,8 @@ rule mirseq_fastqc_pretrim: threads: 1 shell: """ mkdir -p {params.out}/{wildcards.x} - {params.fastqc}/fastqc -o {params.out}/{wildcards.x} {params.indir}/{wildcards.x}.fastq.gz + module load fastqc + fastqc -o {params.out}/{wildcards.x} {params.indir}/{wildcards.x}.fastq.gz """ rule mirseq_fastqc_posttrim: @@ -89,7 +110,8 @@ rule mirseq_fastqc_posttrim: threads: 1 shell: """ mkdir -p {params.out}/{wildcards.x} - {params.fastqc}/fastqc -o {params.out}/{wildcards.x} {params.indir}/{wildcards.x}.cutadapt.fastq + module load fastqc + fastqc -o {params.out}/{wildcards.x} {params.indir}/{wildcards.x}.cutadapt.fastq """ @@ -99,9 +121,12 @@ rule mirseq_mirdeep2_mapper: params: mirdeep=config['bin'][pfamily]['tool_paths']['MIRDEEP2_PATH'],indir=config['project']['workpath']+"/fastqs",out=config['project']['workpath']+"/mirdeep2",mapper_params=config['bin'][pfamily]['tool_parameters']['MAPPER_PARAMS'],bowtie_ref=config['references'][pfamily]['reference_files']['BOWTIE_REF'],mem="16G",time="4:00:00",partition="ccr",rname="mir:mapper" threads: 1 shell: """ - export PATH=/data/dwheeler/CAP-miRSEQ/bin:$PATH +## export PATH=/home/lobanovav/miniconda3/bin:$PATH + export PATH=/home/lobanovav/microRNA/scripts:$PATH + mkdir -p {params.out}/{wildcards.x} - {params.mirdeep}/mapper.pl {input} {params.mapper_params} -p {params.bowtie_ref} -s {params.out}/{wildcards.x}/{wildcards.x}.reads.fa -t {params.out}/{wildcards.x}/{wildcards.x}.reads_vs_genome.arf -o {threads} + module load mirdeep + mapper.pl {input} {params.mapper_params} -p {params.bowtie_ref} -s {params.out}/{wildcards.x}/{wildcards.x}.reads.fa -t {params.out}/{wildcards.x}/{wildcards.x}.reads_vs_genome.arf -o {threads} """ rule mirseq_make_bams: @@ -110,19 +135,22 @@ rule mirseq_make_bams: params: out=config['project']['workpath']+"/bams",bowtie=config['bin'][pfamily]['tool_paths']['BOWTIE_PATH'],bowtie_ref=config['references'][pfamily]['reference_files']['BOWTIE_REF'],bowtie_params=config['bin'][pfamily]['tool_parameters']['BOWTIE_PARAMS'],quals="--phred33-quals",samtools=config['bin'][pfamily]['tool_paths']['SAMTOOLS_PATH'],addorreplacereadgroups_params=config['bin'][pfamily]['tool_parameters']['ADDORREPLACEREADGROUPS_PARAMS'],java_path=config['bin'][pfamily]['tool_paths']['JAVA_PATH'],picard_path=config['bin'][pfamily]['tool_paths']['PICARD_PATH'],addorreplacereadgroups_jvm_mem=config['bin'][pfamily]['java_parameters']['ADDORREPLACEREADGROUPS_JVM_MEM'],script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],mem="32G",time="4:00:00",partition="ccr",rname="mir:bowtie" threads: 1 shell: """ - {params.bowtie}/bowtie {params.quals} {params.bowtie_params} --sam-RG ID:{wildcards.x} --sam-RG SM:{wildcards.x} {params.bowtie_ref} {input} {params.out}/{wildcards.x}.aligned.sam 2> {params.out}/{wildcards.x}.bowtie.log + module load samtools + module load bowtie + module load picard + bowtie {params.quals} {params.bowtie_params} --sam-RG ID:{wildcards.x} --sam-RG SM:{wildcards.x} {params.bowtie_ref} {input} {params.out}/{wildcards.x}.aligned.sam 2> {params.out}/{wildcards.x}.bowtie.log - {params.samtools}/samtools view -SH {params.out}/{wildcards.x}.aligned.sam > {params.out}/{wildcards.x}.aligned.mq.sam + samtools view -SH {params.out}/{wildcards.x}.aligned.sam > {params.out}/{wildcards.x}.aligned.mq.sam - {params.samtools}/samtools view -S {params.out}/{wildcards.x}.aligned.sam | {params.script_path}/dw_setqual.pl >> {params.out}/{wildcards.x}.aligned.mq.sam + samtools view -S {params.out}/{wildcards.x}.aligned.sam | {params.script_path}/dw_setqual.pl >> {params.out}/{wildcards.x}.aligned.mq.sam rm {params.out}/{wildcards.x}.aligned.sam {params.java_path}/java {params.addorreplacereadgroups_jvm_mem} -jar {params.picard_path}/AddOrReplaceReadGroups.jar INPUT={params.out}/{wildcards.x}.aligned.mq.sam OUTPUT={params.out}/{wildcards.x}.bam SORT_ORDER=coordinate TMP_DIR={params.out} RGID={wildcards.x} RGPU={wildcards.x} RGSM={wildcards.x} {params.addorreplacereadgroups_params} rm {params.out}/{wildcards.x}.aligned.mq.sam - {params.samtools}/samtools index {params.out}/{wildcards.x}.bam - {params.samtools}/samtools flagstat {params.out}/{wildcards.x}.bam >{params.out}/{wildcards.x}.bam.flagstat + samtools index {params.out}/{wildcards.x}.bam + samtools flagstat {params.out}/{wildcards.x}.bam >{params.out}/{wildcards.x}.bam.flagstat """ rule mirseq_make_bams_bwa: @@ -132,10 +160,12 @@ rule mirseq_make_bams_bwa: params: out=config['project']['workpath']+"/bams-bwa",samtools=config['bin'][pfamily]['tool_paths']['SAMTOOLS_PATH'],genome=config['references'][pfamily]['reference_files']['REF_GENOME'],mem="32G",time="4:00:00",partition="ccr",rname="mir:bwa" threads: 4 shell: """ - /usr/local/apps/bwa/0.7.10/bwa mem -t {threads} {params.genome} {input} > {params.out}/{wildcards.x}.sam + module load bwa + module load samtools + bwa mem -t {threads} {params.genome} {input} > {params.out}/{wildcards.x}.sam - {params.samtools}/samtools view -Shu {params.out}/{wildcards.x}.sam > {output} - {params.samtools}/samtools flagstat {params.out}/{wildcards.x}.bam > {params.out}/{wildcards.x}.bam.flagstat + samtools view -Shu {params.out}/{wildcards.x}.sam > {output} + samtools flagstat {params.out}/{wildcards.x}.bam > {params.out}/{wildcards.x}.bam.flagstat """ @@ -148,12 +178,17 @@ rule mirseq_mirdeep2: threads: 1 shell: """ -module load viennarna +###module load viennarna module load bowtie/1.1.1 module load randfold module load mirdeep -export PATH=/data/dwheeler/CAP-miRSEQ/bin:$PATH -cd {params.out}/{wildcards.x} && {params.script_path}/miRDeep2.pl {wildcards.x}.reads.fa {params.genome} {wildcards.x}.reads_vs_genome.arf {params.mature} {params.mirdeep2_close_species} {params.precursor} {params.mirdeep2_params} 2>&1|tee mirdeep2.log + +##export PATH=/home/lobanovav/miniconda3/bin:$PATH + export PATH=/home/lobanovav/microRNA/scripts:$PATH + + +##export PATH=/home/lobanovav/miniconda3/bin:$PATH +cd {params.out}/{wildcards.x} && miRDeep2.pl {wildcards.x}.reads.fa {params.genome} {wildcards.x}.reads_vs_genome.arf {params.mature} {params.mirdeep2_close_species} {params.precursor} {params.mirdeep2_params} 2>&1|tee mirdeep2.log # rm -Rf ./dir_prepare_signature* # rm -Rf ./expression_analyses @@ -163,20 +198,20 @@ cd {params.out}/{wildcards.x} && {params.script_path}/miRDeep2.pl {wildcards.x}. """ -rule mirseq_variants: - input: expand("{p}/bams/{x}.bam",x=samples,p=config['project']['workpath']) - output: config['project']['workpath']+"/variants/mirna_variants.vcf" - params: genome=config['references'][pfamily]['reference_files']['REF_GENOME_IUPAC'],out=config['project']['workpath']+"/variants",script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],mirgff=config['references'][pfamily]['reference_files']['MIRBASE_GFF'],bedpath=config['bin'][pfamily]['tool_paths']['BEDTOOLS_PATH'],gatkjar=config['bin'][pfamily]['tool_paths']['GATK_JAR'],unifiedgenotyper_params=config['bin'][pfamily]['tool_parameters']['UNIFIEDGENOTYPER_PARAMS'],vcftools_path=config['bin'][pfamily]['tool_paths']['VCFTOOLS_PATH'],units=expand("{s}",s=samples),java_path=config['bin'][pfamily]['tool_paths']['JAVA_PATH'],unifiedgenotyper_jvm_mem=config['bin'][pfamily]['java_parameters']['UNIFIEDGENOTYPER_JVM_MEM'],vcftools_perllib=config['bin'][pfamily]['tool_paths']['VCFTOOLS_PERLLIB'],mem="16G",time="4:00:00",partition="ccr",rname="mir:variants" - threads: 1 - run: - I=" -I "+" -I ".join(input) - cmd=""" - {params.script_path}/dw_makebeds.sh {params.mirgff} {params.out} {params.bedpath} - {params.java_path}/java {params.unifiedgenotyper_jvm_mem} -jar {params.gatkjar} -T UnifiedGenotyper -R {params.genome} {I} -L {params.out}/mirbase_precursor.tmp.bed -o {params.out}/mirna_variants.vcf {params.unifiedgenotyper_params} - {params.script_path}/dw_annotation_report.sh {params.out} {params.bedpath} {params.vcftools_path} {params.vcftools_perllib} - - {params.script_path}/dw_write_header.sh {params.out} {params.units} - {params.script_path}/dw_merge_annotations.sh {params.out} +##rule mirseq_variants: +## input: expand("{p}/bams/{x}.bam",x=samples,p=config['project']['workpath']) +## output: config['project']['workpath']+"/variants/mirna_variants.vcf" +## params: genome=config['references'][pfamily]['reference_files']['REF_GENOME_IUPAC'],out=config['project']['workpath']+"/variants",script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],mirgff=config['references'][pfamily]['reference_files']['MIRBASE_GFF'],bedpath=config['bin'][pfamily]['tool_paths']['BEDTOOLS_PATH'],gatkjar=config['bin'][pfamily]['tool_paths']['GATK_JAR'],unifiedgenotyper_params=config['bin'][pfamily]['tool_parameters']['UNIFIEDGENOTYPER_PARAMS'],vcftools_path=config['bin'][pfamily]['tool_paths']['VCFTOOLS_PATH'],units=expand("{s}",s=samples),java_path=config['bin'][pfamily]['tool_paths']['JAVA_PATH'],unifiedgenotyper_jvm_mem=config['bin'][pfamily]['java_parameters']['UNIFIEDGENOTYPER_JVM_MEM'],vcftools_perllib=config['bin'][pfamily]['tool_paths']['VCFTOOLS_PERLLIB'],mem="16G",time="4:00:00",partition="ccr",rname="mir:variants" +## threads: 1 +## run: +## I=" -I "+" -I ".join(input) +## cmd=""" +## {params.script_path}/dw_makebeds.sh {params.mirgff} {params.out} {params.bedpath} +## {params.java_path}/java {params.unifiedgenotyper_jvm_mem} -jar {params.gatkjar} -T UnifiedGenotyper -R {params.genome} {I} -L {params.out}/mirbase_precursor.tmp.bed -o {params.out}/mirna_variants.vcf {params.unifiedgenotyper_params} +## {params.script_path}/dw_annotation_report.sh {params.out} {params.bedpath} {params.vcftools_path} {params.vcftools_perllib} +## +## {params.script_path}/dw_write_header.sh {params.out} {params.units} +## {params.script_path}/dw_merge_annotations.sh {params.out} # rm $output_dir/mirbase_precursor.tmp.bed # rm $output_dir/mirbase_mature.tmp.bed @@ -190,23 +225,23 @@ rule mirseq_variants: # rm $output_dir/mirna_variants.vcf.txt # rm $output_dir/mirna_variants.vcf.txt.bed # -""" - shell(cmd) +##""" +## shell(cmd) -rule mirseq_gencode_classification: - input: config['project']['workpath']+"/bams/{x}.bam" - output: config['project']['workpath']+"/qc/other_rna/{x}.gencode.genecount.txt" - params: java_path=config['bin'][pfamily]['tool_paths']['JAVA_PATH'],sortsam_jvm_mem=config['bin'][pfamily]['java_parameters']['SORTSAM_JVM_MEM'],picard_path=config['bin'][pfamily]['tool_paths']['PICARD_PATH'],input_dir=config['project']['workpath']+"/bams",out=config['project']['workpath']+"/qc/other_rna",sortsam_params=config['bin'][pfamily]['tool_parameters']['SORTSAM_PARAMS'],htseq_path=config['bin'][pfamily]['tool_paths']['HTSEQ_PATH'],htseq_params=config['bin'][pfamily]['tool_parameters']['HTSEQ_PARAMS'],gencode_gtf=config['references'][pfamily]['reference_files']['GENCODE_GTF'],script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],python_path=config['bin'][pfamily]['tool_paths']['PYTHON_PATH'],htseq_lib_path=config['bin'][pfamily]['tool_paths']['HTSEQ_LIB_PATH'],samtools_path=config['bin'][pfamily]['tool_paths']['SAMTOOLS_PATH'],rscript_path=config['bin'][pfamily]['tool_paths']['RSCRIPT_PATH'],mem="16G",time="4:00:00",partition="ccr",rname="mir:classify" - threads: 1 - shell: """ +##rule mirseq_gencode_classification: +## input: config['project']['workpath']+"/bams/{x}.bam" +## output: config['project']['workpath']+"/qc/other_rna/{x}.gencode.genecount.txt" +## params: java_path=config['bin'][pfamily]['tool_paths']['JAVA_PATH'],sortsam_jvm_mem=config['bin'][pfamily]['java_parameters']['SORTSAM_JVM_MEM'],picard_path=config['bin'][pfamily]['tool_paths']['PICARD_PATH'],input_dir=config['project']['workpath']+"/bams",out=config['project']['workpath']+"/qc/other_rna",sortsam_params=config['bin'][pfamily]['tool_parameters']['SORTSAM_PARAMS'],htseq_path=config['bin'][pfamily]['tool_paths']['HTSEQ_PATH'],htseq_params=config['bin'][pfamily]['tool_parameters']['HTSEQ_PARAMS'],gencode_gtf=config['references'][pfamily]['reference_files']['GENCODE_GTF'],script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],python_path=config['bin'][pfamily]['tool_paths']['PYTHON_PATH'],htseq_lib_path=config['bin'][pfamily]['tool_paths']['HTSEQ_LIB_PATH'],samtools_path=config['bin'][pfamily]['tool_paths']['SAMTOOLS_PATH'],rscript_path=config['bin'][pfamily]['tool_paths']['RSCRIPT_PATH'],mem="16G",time="4:00:00",partition="ccr",rname="mir:classify" +## threads: 1 +## shell: """ -{params.java_path}/java {params.sortsam_jvm_mem} -jar {params.picard_path}/SortSam.jar INPUT={params.input_dir}/{wildcards.x}.bam OUTPUT={params.out}/{wildcards.x}.queryname.bam SORT_ORDER=queryname TMP_DIR={params.out}/ {params.sortsam_params} +##{params.java_path}/java {params.sortsam_jvm_mem} -jar {params.picard_path}/SortSam.jar INPUT={params.input_dir}/{wildcards.x}.bam OUTPUT={params.out}/{wildcards.x}.queryname.bam SORT_ORDER=queryname TMP_DIR={params.out}/ {params.sortsam_params} -{params.samtools_path}/samtools view {params.out}/{wildcards.x}.queryname.bam | {params.htseq_path}/htseq-count {params.htseq_params} - {params.gencode_gtf} > {params.out}/{wildcards.x}.gencode.genecount.txt +##{params.samtools_path}/samtools view {params.out}/{wildcards.x}.queryname.bam | {params.htseq_path}/htseq-count {params.htseq_params} - {params.gencode_gtf} > {params.out}/{wildcards.x}.gencode.genecount.txt -{params.script_path}/dw_gencode.sh {params.python_path} {params.htseq_lib_path} {params.gencode_gtf} {params.out} {wildcards.x} {params.script_path} {params.rscript_path} +##{params.script_path}/dw_gencode.sh {params.python_path} {params.htseq_lib_path} {params.gencode_gtf} {params.out} {wildcards.x} {params.script_path} {params.rscript_path} - """ +## """ rule mirseq_expression_reports: input: expand("{out}/mirdeep2/{x}/mirdeep2.log",x=samples,out=config['project']['workpath']) @@ -263,42 +298,43 @@ rule mirseq_main_document: shell("{params.script_path}/dw_main_document.sh {params.out} {params.script_path} {params.flowcell} {params.tool} {params.call_snvs} {params.trim_adapter} {params.diff_expression} {params.diff_expression_analyses} {params.email};perl {params.script_path}/dw_create_igv.pl {params.out}/igv {params.samples} {params.delivery_folder} {params.tool_info} {params.server} {params.genome_build};cp {params.script_path}/IGV_Setup.doc {params.out}/igv;perl {params.script_path}/dw_main_document.pl {params.out}/pfamily.tmp {params.out}/MainDocument.html {params.out}/SampleSummary.xls {snvs} {trim} {diff};cp {params.script_path}/CAP-miRSeq_workflow.png {params.out}") -rule mirseq_miRspring_bowtie: - input: config['project']['workpath']+"/bams/{x}.bam" - output: config['project']['workpath']+"/mirspring/{x}.html" - params: script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],output=config['project']['workpath'],mirbase_files=config['references'][pfamily]['reference_files']['MIRBASE_FILES'],mem="16G",time="4:00:00",partition="ccr",rname="mir:mirspring" - shell: """ - if [ ! -d {params.output}/mirspring ] - then - mkdir {params.output}/mirspring - fi +##rule mirseq_miRspring_bowtie: +## input: config['project']['workpath']+"/bams/{x}.bam" +## output: config['project']['workpath']+"/mirspring/{x}.html" +## params: script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],output=config['project']['workpath'],mirbase_files=config['references'][pfamily]['reference_files']['MIRBASE_FILES'],mem="16G",time="4:00:00",partition="ccr",rname="mir:mirspring" +## shell: """ +## if [ ! -d {params.output}/mirspring ] +## then +## mkdir {params.output}/mirspring +## fi - cd {params.script_path} && perl {params.script_path}/BAM_to_Intermediate.pl -ml 0 -s hsa -pre {params.mirbase_files}/hsa.35nt.fasta -gff {params.mirbase_files}/hsa_dw.gff3 -mat {params.mirbase_files}/mature.fa -bam {params.output}/bams/{wildcards.x}.bam -ref 0 -out {params.output}/mirspring/{wildcards.x}.tmp.txt -flank 35 +## cd {params.script_path} && perl {params.script_path}/BAM_to_Intermediate.pl -ml 0 -s hsa -pre {params.mirbase_files}/hsa.35nt.fasta -gff {params.mirbase_files}/hsa_dw.gff3 -mat {params.mirbase_files}/mature.fa -bam {params.output}/bams/{wildcards.x}.bam -ref 0 -out {params.output}/mirspring/{wildcards.x}.tmp.txt -flank 35 - cd {params.script_path} && perl {params.script_path}/Intermediate_to_miRspring.pl -in {params.output}/mirspring/{wildcards.x}.tmp.txt -s hsa -ref 0 -mat {params.mirbase_files}/mature.fa -out {params.output}/mirspring/{wildcards.x}.html -flank 35 - """ +## cd {params.script_path} && perl {params.script_path}/Intermediate_to_miRspring.pl -in {params.output}/mirspring/{wildcards.x}.tmp.txt -s hsa -ref 0 -mat {params.mirbase_files}/mature.fa -out {params.output}/mirspring/{wildcards.x}.html -flank 35 +## """ -rule mirseq_miRspring_bwa: - input: config['project']['workpath']+"/bams-bwa/{x}.bam" - output: config['project']['workpath']+"/mirspring/{x}_bwa.html" - params: script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],output=config['project']['workpath'],mirbase_files=config['references'][pfamily]['reference_files']['MIRBASE_FILES'],mem="16G",time="4:00:00",partition="ccr",rname="mir:mirspring" - shell: """ - if [ ! -d {params.output}/mirspring ] - then - mkdir {params.output}/mirspring - fi +##rule mirseq_miRspring_bwa: +## input: config['project']['workpath']+"/bams-bwa/{x}.bam" +## output: config['project']['workpath']+"/mirspring/{x}_bwa.html" +## params: script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],output=config['project']['workpath'],mirbase_files=config['references'][pfamily]['reference_files']['MIRBASE_FILES'],mem="16G",time="4:00:00",partition="ccr",rname="mir:mirspring" +## shell: """ +## if [ ! -d {params.output}/mirspring ] +## then +## mkdir {params.output}/mirspring +## fi - cd {params.script_path} && perl {params.script_path}/BAM_to_Intermediate.pl -ml 0 -s hsa -pre {params.mirbase_files}/hsa.35nt.fasta -gff {params.mirbase_files}/hsa_dw.gff3 -mat {params.mirbase_files}/mature.fa -bam {params.output}/bams-bwa/{wildcards.x}.bam -ref 0 -out {params.output}/mirspring/{wildcards.x}_bwa.tmp.txt -flank 35 +## cd {params.script_path} && perl {params.script_path}/BAM_to_Intermediate.pl -ml 0 -s hsa -pre {params.mirbase_files}/hsa.35nt.fasta -gff {params.mirbase_files}/hsa_dw.gff3 -mat {params.mirbase_files}/mature.fa -bam {params.output}/bams-bwa/{wildcards.x}.bam -ref 0 -out {params.output}/mirspring/{wildcards.x}_bwa.tmp.txt -flank 35 - cd {params.script_path} && perl {params.script_path}/Intermediate_to_miRspring.pl -in {params.output}/mirspring/{wildcards.x}_bwa.tmp.txt -s hsa -ref 0 -mat {params.mirbase_files}/mature.fa -out {params.output}/mirspring/{wildcards.x}_bwa.html -flank 35 - """ -rule mirseq_targetscan: - input: - output: - params: script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],output=config['project']['workpath'],target_data=config['references'][pfamily]['reference_files']['TARGET_DATA'],mem="4G",time="4:00:00",partition="ccr",rname="mir:tscan" - shell: """ +## cd {params.script_path} && perl {params.script_path}/Intermediate_to_miRspring.pl -in {params.output}/mirspring/{wildcards.x}_bwa.tmp.txt -s hsa -ref 0 -mat {params.mirbase_files}/mature.fa -out {params.output}/mirspring/{wildcards.x}_bwa.html -flank 35 +## """ +##rule mirseq_targetscan: +## input: +## output: +## params: script_path=config['bin'][pfamily]['tool_paths']['SCRIPT_PATH'],output=config['project']['workpath'],target_data=config['references'][pfamily]['reference_files']['TARGET_DATA'],mem="4G",time="4:00:00",partition="ccr",rname="mir:tscan" +## shell: """ - {params.script_path}/targetscan_70.pl {params.target_data}/miR_Family_info_sample.txt {params.target_data}/UTR_sequences_all.txt {params.output}/targetscan_70_output.txt +## {params.script_path}/targetscan_70.pl {params.target_data}/miR_Family_info_sample.txt {params.target_data}/UTR_sequences_all.txt {params.output}/targetscan_70_output.txt - """ +## """ + diff --git a/gui/frame.py b/gui/frame.py index 7ce4137..d584734 100644 --- a/gui/frame.py +++ b/gui/frame.py @@ -65,13 +65,13 @@ def __init__( self, parent, pipeline_name, annotation, *args, **kwargs ) : self.dry_button = dry_button = Button(self, text="Dry Run", command=self.dryrun, - state='disabled' ) + state='active' ) dry_button.grid(row=4, column=4, sticky=E) self.run_button = run_button = Button(self, text="Run", command=self.runslurm, - state='disabled' ) + state='active' ) run_button.grid( row=4, column=5 ) data_entry = Entry(pipepanel, @@ -79,7 +79,7 @@ def __init__( self, parent, pipeline_name, annotation, *args, **kwargs ) : width = 50, #bg = entryBgColor, #fg = entryFgColor, - textvariable = datapath, state='readonly' + textvariable = datapath, state='normal' ) self.work_entry = work_entry = Entry(pipepanel, @@ -87,7 +87,7 @@ def __init__( self, parent, pipeline_name, annotation, *args, **kwargs ) : width=50, #bg=entryBgColor, #fg=entryFgColor, - textvariable=workpath, state='readonly' + textvariable=workpath, state='normal' ) data_entry.grid( row=1, column=2, columnspan=3 ) @@ -111,7 +111,7 @@ def __init__( self, parent, pipeline_name, annotation, *args, **kwargs ) : command=self.init_work_dir ) work_button.grid( row=4, column=3 ) - work_button.config( state="disabled" ) #( "disabled" ) + work_button.config( state="active" ) #( "disabled" ) def set_data_directory( self ): diff --git a/gui/rnaseq.py b/gui/rnaseq.py index d8ff0b8..4e226ce 100644 --- a/gui/rnaseq.py +++ b/gui/rnaseq.py @@ -91,9 +91,9 @@ def __init__(self, pipepanel, pipeline_name, *args, **kwargs) : #rMincount.trace('w', lambda a,b,c,x="rmincount": makejson(x)) #Filter out genes < [5] read counts in < [2] samples - rminsamplesL = Label(sampleLF, text="Filter out genes <") # in") + rminsamplesL = Label(sampleLF, text="Include genes with >=") # in") rmincountE = Entry(sampleLF, bd =2, width=3, textvariable=rMincount) - rmincountL = Label(sampleLF, text="read counts in >") + rmincountL = Label(sampleLF, text="read counts in >=") rminsamplesE = Entry(sampleLF, bd =2, width=3, textvariable=rMinsamples) rminsamplesR = Label(sampleLF, text="samples") @@ -392,4 +392,4 @@ def makejson(self, *args): gi.jsonconf.insert(INSERT, J) self.saveproject(gi.jsonconf.get("1.0",END)) - \ No newline at end of file +