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1 process TABLE_SUMMARY {
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2 tag "$table_sum_on"
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3 label 'process_micro'
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4
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5 // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
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6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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7 conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pyyaml conda-forge::coreutils" : null)
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8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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9 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
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10 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
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11
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12 input:
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13 tuple val(table_sum_on), path(tables)
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14
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15 output:
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16 tuple val(table_sum_on), path("*.tblsum.txt"), emit: tblsummed
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17 path "*_mqc.yml" , emit: mqc_yml
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18 path "versions.yml" , emit: versions
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19
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20 when:
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21 task.ext.when == null || task.ext.when || tables
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 def onthese = tables.collect().join('\\n')
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26 """
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27 filenum="1"
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28 header=""
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29
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30 echo -e "$onthese" | while read -r file; do
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31
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32 if [ "\${filenum}" == "1" ]; then
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33 header=\$( head -n1 "\${file}" )
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34 echo -e "\${header}" > ${table_sum_on}.tblsum.txt
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35 fi
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36
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37 tail -n+2 "\${file}" >> ${table_sum_on}.tblsum.txt
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38
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39 filenum=\$((filenum+1))
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40 done
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41
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42 create_mqc_data_table.py $table_sum_on
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43
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44 cat <<-END_VERSIONS > versions.yml
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45 "${task.process}":
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46 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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47 python: \$( python --version | sed 's/Python //g' )
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48 END_VERSIONS
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49
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50 headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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51 tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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52
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53 cat <<-END_VERSIONS >> versions.yml
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54 head: \$headver
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55 tail: \$tailver
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56 END_VERSIONS
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57 """
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58 } |
