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1 process SEQKIT_RMDUP {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null)
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6 conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
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9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
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10
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11 input:
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12 tuple val(meta), path(reads)
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13
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14 output:
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15 tuple val(meta), path("*duplicated.details.txt"), optional: true
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16 tuple val(meta), path("*.gz") , emit: fastx
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 def rmdup_d = params.seqkit_rmdup_d ? "-d ${prefix}.seqs.duplicated.fastq.gz" : ""
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26 def rmdup_D = params.seqkit_rmdup_D ? "-D ${prefix}.duplicated.details.txt" : ""
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27
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28 def extension = "fastq"
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29 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
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30 extension = "fasta"
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31 }
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32
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33 if (meta.single_end) {
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34 """
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35 seqkit \\
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36 rmdup \\
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37 $rmdup_d \\
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38 $rmdup_D \\
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39 -j $task.cpus \\
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40 -o ${prefix}.seqkit-rmdup.${extension}.gz \\
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41 $args \\
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42 $reads
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43
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44 cat <<-END_VERSIONS > versions.yml
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45 "${task.process}":
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46 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
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47 END_VERSIONS
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48 """
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49 } else {
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50 """
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51 seqkit \\
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52 rmdup \\
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53 $rmdup_d \\
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54 $rmdup_D \\
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55 -j $task.cpus \\
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56 -o ${prefix}.R1.seqkit-rmdup.${extension}.gz \\
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57 $args \\
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58 ${reads[0]}
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59
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60 seqkit \\
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61 rmdup \\
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62 $rmdup_d \\
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63 $rmdup_D \\
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64 -j $task.cpus \\
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65 -o ${prefix}.R2.seqkit-rmdup.${extension}.gz \\
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66 $args \\
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67 ${reads[1]}
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68
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69 seqkit \\
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70 pair \\
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71 -j $task.cpus \\
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72 -1 ${prefix}.R1.seqkit-rmdup.${extension}.gz \\
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73 -2 ${prefix}.R2.seqkit-rmdup.${extension}.gz
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74
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75 rm ${prefix}.R1.seqkit-rmdup.${extension}.gz
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76 rm ${prefix}.R2.seqkit-rmdup.${extension}.gz
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77
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78 cat <<-END_VERSIONS > versions.yml
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79 "${task.process}":
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80 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
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81 END_VERSIONS
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82 """
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83 }
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84 }
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