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Merge pull request #156 from CKComputomics/contaminationFiltering
Contamination filtering
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| process BLAT_MIRNA { | ||
| tag "$fasta" | ||
| label 'process_medium' | ||
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| conda (params.enable_conda ? 'bioconda::blat=36' : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/blat:36--0' : | ||
| 'quay.io/biocontainers/blat:36--0' }" | ||
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| input: | ||
| val db_type | ||
| path mirna | ||
| path contaminants | ||
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| output: | ||
| path 'filtered.fa' , emit: filtered_set | ||
| path "versions.yml" , emit: versions | ||
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| script: | ||
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| if ( db_type == "cdna" ) | ||
| """ | ||
| echo $db_type | ||
| awk '/^>/ { x=index(\$6, "transcript_biotype:miRNA") } { if(!x) print }' $contaminants > subset.fa | ||
| blat -out=blast8 $mirna subset.fa /dev/stdout | awk 'BEGIN{FS="\t"}{if(\$11 < 1e-5)print \$1;}' | uniq > mirnahit.txt | ||
| awk 'BEGIN { while((getline<"mirnahit.txt")>0) l[">"\$1]=1 } /^>/ {x = l[\$1]} {if(!x) print }' subset.fa > filtered.fa | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blat: \$(echo \$(blat) | grep Standalone | awk '{ if (match(\$0,/[0-9]*[0-9]/,m)) print m[0] }') | ||
| END_VERSIONS | ||
| """ | ||
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| else if ( db_type == "ncrna" ) | ||
| """ | ||
| echo $db_type | ||
| awk '/^>/ { x=(index(\$6, "transcript_biotype:rRNA") || index(\$6, "transcript_biotype:miRNA")) } { if(!x) print }' $contaminants > subset.fa | ||
| blat -out=blast8 $mirna subset.fa /dev/stdout | awk 'BEGIN{FS="\t"}{if(\$11 < 1e-5)print \$1;}' | uniq > mirnahit.txt | ||
| awk 'BEGIN { while((getline<"mirnahit.txt")>0) l[">"\$1]=1 } /^>/ {x = l[\$1]} {if(!x) print }' subset.fa > filtered.fa | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blat: \$(echo \$(blat) | grep Standalone | awk '{ if (match(\$0,/[0-9]*[0-9]/,m)) print m[0] }') | ||
| END_VERSIONS | ||
| """ | ||
|
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| else | ||
| """ | ||
| echo $db_type | ||
| blat -out=blast8 $mirna $contaminants /dev/stdout | awk 'BEGIN{FS="\t"}{if(\$11 < 1e-5)print \$1;}' | uniq > mirnahit.txt | ||
| awk 'BEGIN { while((getline<"mirnahit.txt")>0) l[">"\$1]=1 } /^>/ {x = l[\$1]} {if(!x) print }' $contaminants > filtered.fa | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blat: \$(echo \$(blat) | grep Standalone | awk '{ if (match(\$0,/[0-9]*[0-9]/,m)) print m[0] }') | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| process INDEX_CONTAMINANTS { | ||
| label 'process_medium' | ||
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| conda (params.enable_conda ? 'bowtie2=2.4.5' : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2' : | ||
| 'quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2' }" | ||
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| input: | ||
| path fasta | ||
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| output: | ||
| path 'fasta_bidx*' , emit: bt_indices | ||
| path "versions.yml" , emit: versions | ||
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| script: | ||
| """ | ||
| bowtie2-build ${fasta} fasta_bidx --threads ${task.cpus} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//') | ||
| END_VERSIONS | ||
| """ | ||
|
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||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| process BOWTIE_MAP_CONTAMINANTS { | ||
| label 'process_medium' | ||
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| conda (params.enable_conda ? 'bowtie2=2.4.5' : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2' : | ||
| 'quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2' }" | ||
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| input: | ||
| tuple val(meta), path(reads) | ||
| path index | ||
| val contaminant_type | ||
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| output: | ||
| tuple val(meta), path("*sam") , emit: bam | ||
| tuple val(meta), path('*.filter.unmapped.contaminant.fastq'), emit: unmapped | ||
| path "versions.yml" , emit: versions | ||
| path "filtered.*.stats" , emit: stats | ||
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| script: | ||
| def index_base = index.toString().tokenize(' ')[0].tokenize('.')[0] | ||
| """ | ||
| bowtie2 \\ | ||
| --threads ${task.cpus} \\ | ||
| --very-sensitive-local \\ | ||
| -k 1 \\ | ||
| -x $index_base \\ | ||
| --un ${meta.id}.${contaminant_type}.filter.unmapped.contaminant.fastq \\ | ||
| ${reads} \\ | ||
| -S ${meta.id}.filter.contaminant.sam > ${meta.id}.contaminant_bowtie.log 2>&1 | ||
| # extracting number of reads from bowtie logs | ||
| awk -v type=${contaminant_type} 'BEGIN{tot=0} {if(NR==4 || NR == 5){tot += \$1}} END {print "\\""type"\\": "tot }' ${meta.id}.contaminant_bowtie.log | tr -d , > filtered.${meta.id}_${contaminant_type}.stats | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' | tr -d '\0') | ||
| END_VERSIONS | ||
| """ | ||
|
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||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| process FILTER_STATS { | ||
| label 'process_medium' | ||
|
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||
| conda (params.enable_conda ? 'bowtie2=2.4.5' : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2' : | ||
| 'quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2' }" | ||
|
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| input: | ||
| tuple val(meta), path(reads) | ||
| path stats_files | ||
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| output: | ||
| path "*_mqc.yaml" , emit: stats | ||
| tuple val(meta), path('*.filtered.fastq.gz') , emit: reads | ||
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| script: | ||
| """ | ||
| readnumber=\$(wc -l ${reads} | awk '{ print \$1/4 }') | ||
| cat ./filtered.${meta.id}_*.stats | \\ | ||
| tr '\n' ', ' | \\ | ||
| awk -v sample=${meta.id} -v readnumber=\$readnumber '{ print "id: \\"my_pca_section\\"\\nsection_name: \\"Contamination Filtering\\"\\ndescription: \\"This plot shows the amount of reads filtered by contaminant type.\\"\\nplot_type: \\"bargraph\\"\\npconfig:\\n id: \\"contamination_filter_plot\\"\\n title: \\"Contamination Plot\\"\\n ylab: \\"Number of reads\\"\\ndata:\\n "sample": {"\$0"\\"remaining reads\\": "readnumber"}" }' > ${meta.id}.contamination_mqc.yaml | ||
| gzip -c ${reads} > ${meta.id}.filtered.fastq.gz | ||
| """ | ||
| } |
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