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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| process phage_references_blastDB { | ||
| if (params.cloudProcess) { | ||
| publishDir "${params.cloudDatabase}/", mode: 'copy', pattern: "blast_phage_DB" | ||
| } | ||
| else { | ||
| storeDir "nextflow-autodownload-databases/" | ||
| } | ||
| label 'metaphinder' | ||
| input: | ||
| file(references) | ||
| output: | ||
| file("blast_phage_DB/") | ||
| script: | ||
| """ | ||
| makeblastdb -in ${references} -dbtype nucl -parse_seqids -out blast_phage_DB/phage_db -title phage_db | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| process filter_metaphinder { | ||
| publishDir "${params.output}/${name}/metaphinder", mode: 'copy', pattern: "metaphinder_*.txt" | ||
| label 'ubuntu' | ||
| input: | ||
| tuple val(name), file(results) | ||
| output: | ||
| tuple val(name), file("metaphinder_*.txt") | ||
| script: | ||
| """ | ||
| rnd=${Math.random()} | ||
| cat *.list | sort -g -k4,4 | awk '{if(\$2=="phage"){print \$1}}' | tail -n+2 > metaphinder_\${rnd//0.}.txt | ||
| """ | ||
| } | ||
|
|
||
| process filter_metaphinder_own_DB { | ||
| publishDir "${params.output}/${name}/metaphinder-own-DB", mode: 'copy', pattern: "metaphinder-own-DB_*.txt" | ||
| label 'ubuntu' | ||
| input: | ||
| tuple val(name), file(results) | ||
| output: | ||
| tuple val(name), file("metaphinder-own-DB_*.txt") | ||
| script: | ||
| """ | ||
| rnd=${Math.random()} | ||
| cat *.list | sort -g -k4,4 | awk '{if(\$2=="phage"){print \$1}}' | tail -n+2 > metaphinder-own-DB_\${rnd//0.}.txt | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| process shuffle_reads_nts { | ||
| //publishDir "${params.output}/${name}/sh", mode: 'copy', pattern: "${name}_pos_ctg.fa" | ||
| label 'ruby' | ||
| input: | ||
| tuple val(name), file(reads) | ||
| output: | ||
| tuple val(name), file("${name}_shuffled.fastq") | ||
| script: | ||
| """ | ||
| #!/usr/bin/env ruby | ||
| fastq = File.open("${reads}", 'r') | ||
| shuffled = File.open("${name}_shuffled.fastq", 'w') | ||
| i = 0 | ||
| out = '' | ||
| fastq.each do |line| | ||
| i += 1 | ||
| if i == 1 || i == 3 || i == 4 | ||
| out << line | ||
| end | ||
| if i == 2 | ||
| out << line.chomp.split("").shuffle.join << "\\n" | ||
| end | ||
| if i == 4 | ||
| shuffled << out if out.length > 1 | ||
| out = '' | ||
| end | ||
| end | ||
| shuffled.close | ||
| fastq.close | ||
| """ | ||
| } | ||
|
|
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