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Configure multiqc to extract and display gfastats results of each tan…
…tan, windowmasker, repeatmasker.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| process CUSTOMMODULE { | ||
| label 'process_single' | ||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/jq:1.6': | ||
| 'biocontainers/jq:1.6' }" | ||
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| input: | ||
| path (assemt) | ||
| path (assemw) | ||
| path (assemr) | ||
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| output: | ||
| path "*_mqc.tsv", emit: tsv | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| """ | ||
| echo "# id: 'tantan repeat summary'" > tantanmqc_mqc.tsv | ||
| echo "# section_name: 'tantan repeat masking summary statistics'" >> tantanmqc_mqc.tsv | ||
| echo "# format: 'tsv'" >> tantanmqc_mqc.tsv | ||
| echo "# plot_type: 'heatmap'" >> tantanmqc_mqc.tsv | ||
| echo "# description: 'This plot shows a brief summary of each genomes whose repeats has been masked'" >> tantanmqc_mqc.tsv | ||
| echo "# pconfig:" >> tantanmqc_mqc.tsv | ||
| echo "# id: 'tantan repeat summary'" >> tantanmqc_mqc.tsv | ||
| echo "# title: 'tantan repeat summary'" >> tantanmqc_mqc.tsv | ||
| echo "# ylab: ''" >> tantanmqc_mqc.tsv | ||
| echo "id\tTotal scaffold length\tTotal contig length\tsoft masked bases" >> tantanmqc_mqc.tsv | ||
| for i in $assemt | ||
| do | ||
| printf "\$(basename \$i .assembly_summary)\t" >>tantanmqc_mqc.tsv | ||
| grep 'Total scaffold length' \$i | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> tantanmqc_mqc.tsv | ||
| grep 'Total contig length' \$i | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> tantanmqc_mqc.tsv | ||
| grep 'soft-masked bases' \$i | tail -n 1 | awk '{print \$4}' >> tantanmqc_mqc.tsv | ||
| done | ||
| echo "# id: 'windowmasker repeat summary'" > windowmqc_mqc.tsv | ||
| echo "# section_name: 'windowmasker repeat masking summary statistics'" >> windowmqc_mqc.tsv | ||
| echo "# format: 'tsv'" >> windowmqc_mqc.tsv | ||
| echo "# plot_type: 'heatmap'" >> windowmqc_mqc.tsv | ||
| echo "# description: 'This plot shows a brief summary of each genomes whose repeats has been masked'" >> windowmqc_mqc.tsv | ||
| echo "# pconfig:" >> windowmqc_mqc.tsv | ||
| echo "# id: 'windowmasker repeat summary'" >> windowmqc_mqc.tsv | ||
| echo "# title: 'windowmasker repeat summary'" >> windowmqc_mqc.tsv | ||
| echo "# ylab: ''" >> windowmqc_mqc.tsv | ||
| echo "id\tTotal scaffold length\tTotal contig length\tsoft masked bases" >> windowmqc_mqc.tsv | ||
| for i in $assemw | ||
| do | ||
| printf "\$(basename \$i .assembly_summary)\t" >> windowmqc_mqc.tsv | ||
| grep 'Total scaffold length' \$i | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> windowmqc_mqc.tsv | ||
| grep 'Total contig length' \$i | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> windowmqc_mqc.tsv | ||
| grep 'soft-masked bases' \$i | tail -n 1 | awk '{print \$4}' >> windowmqc_mqc.tsv | ||
| done | ||
| echo "# id: 'repeatmasker repeat summary'" > repeatmaskmqc_mqc.tsv | ||
| echo "# section_name: 'repeatmasker repeat masking summary statistics'" >> repeatmaskmqc_mqc.tsv | ||
| echo "# format: 'tsv'" >> repeatmaskmqc_mqc.tsv | ||
| echo "# plot_type: 'heatmap'" >> repeatmaskmqc_mqc.tsv | ||
| echo "# description: 'This plot shows a brief summary of each genomes whose repeats has been masked'" >> repeatmaskmqc_mqc.tsv | ||
| echo "# pconfig:" >> repeatmaskmqc_mqc.tsv | ||
| echo "# id: 'repeatmasker repeat summary'" >> repeatmaskmqc_mqc.tsv | ||
| echo "# title: 'repeatmasker repeat summary'" >> repeatmaskmqc_mqc.tsv | ||
| echo "# ylab: ''" >> repeatmaskmqc_mqc.tsv | ||
| echo "id\tTotal scaffold length\tTotal contig length\tsoft masked bases" >> repeatmaskmqc_mqc.tsv | ||
| for i in $assemr | ||
| do | ||
| printf "\$(basename \$i .assembly_summary)\t" >> repeatmaskmqc_mqc.tsv | ||
| grep 'Total scaffold length' \$i | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> repeatmaskmqc_mqc.tsv | ||
| grep 'Total contig length' \$i | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> repeatmaskmqc_mqc.tsv | ||
| grep 'soft-masked bases' \$i | tail -n 1 | awk '{print \$4}' >> repeatmaskmqc_mqc.tsv | ||
| done | ||
| """ | ||
| } |
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