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* skeleton on kmerfinder task * remove kmerfinder_db_name * still trying to get kmerfinder to run * is this working now?!? * first working version of kmerfinder task * parse top hit * make results output file optional * final version of task (for now..) * add kmerfinder_bacteria to theiaprok! * fix typo * pass empty file for tests - kmerfinder_db * fix input json * add kmerfinder query coverage to theiaprok SE, PE, FASTA and ONT * remove undeeded skip on kmerfinder (set to false by default) * fix ops * update md5sum (part1) * update md5sum (part2) * fiz sister typo * missed a file * update CI * add kmerfinder_template_coverage to theiaprok output * expose database name on kmerfinder outputs * update md5sum * fix bug - headers being outputed to datatable
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| version 1.0 | ||
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| task kmerfinder_bacteria { | ||
| input { | ||
| File assembly | ||
| String samplename | ||
| File kmerfinder_db = "gs://theiagen-public-files-rp/terra/theiaprok-files/kmerfinder_bacteria_20230911.tar.gz" | ||
| String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/kmerfinder:3.0.2--hdfd78af_0" | ||
| Int memory = 32 | ||
| Int cpu = 4 | ||
| Int disk_size = 100 | ||
| String kmerfinder_args = "" | ||
| } | ||
| command <<< | ||
| # Decompress the kmerfinder bacterial database | ||
| mkdir db | ||
| tar -C ./db/ -xzvf ~{kmerfinder_db} | ||
|
|
||
| # Run kmerfinder | ||
| kmerfinder.py \ | ||
| -db ./db/bacteria/bacteria.ATG \ | ||
| -tax ./db/bacteria/bacteria.tax \ | ||
| -i ~{assembly} \ | ||
| -o ~{samplename} \ | ||
| ~{kmerfinder_args} | ||
|
|
||
| # parse outputs | ||
| if [ ! -f ~{samplename}/results.txt ]; then | ||
| PF="No hit detected in database" | ||
| QC="No hit detected in database" | ||
| TC="No hit detected in database" | ||
| else | ||
| PF="$(cat ~{samplename}/results.txt | head -n 2 | tail -n 1 | cut -f 19)" | ||
| QC="$(cat ~{samplename}/results.txt | head -n 2 | tail -n 1 | cut -f 6)" | ||
| TC="$(cat ~{samplename}/results.txt | head -n 2 | tail -n 1 | cut -f 7)" | ||
| # String is empty or just contains the header | ||
| if [ "$PF" == "" ] || [ "$PF" == "Species" ]; then | ||
| PF="No hit detected in database" | ||
| QC="No hit detected in database" | ||
| TC="No hit detected in database" | ||
| fi | ||
| mv -v ~{samplename}/results.txt ~{samplename}_kmerfinder.tsv | ||
| fi | ||
| echo $PF | tee TOP_HIT | ||
| echo $QC | tee QC_METRIC | ||
| echo $TC | tee TEMPLATE_COVERAGE | ||
|
|
||
| # extract database name | ||
| DB=$(basename ~{kmerfinder_db} | sed 's/\.tar\.gz$//') | ||
| echo $DB | tee DATABASE | ||
| >>> | ||
| output { | ||
| String kmerfinder_docker = docker | ||
| File? kmerfinder_results_tsv = "~{samplename}_kmerfinder.tsv" | ||
| String kmerfinder_top_hit = read_string("TOP_HIT") | ||
| String kmerfinder_query_coverage = read_string("QC_METRIC") | ||
| String kmerfinder_template_coverage = read_string("TEMPLATE_COVERAGE") | ||
| String kmerfinder_database = read_string("DATABASE") | ||
| } | ||
| runtime { | ||
| docker: docker | ||
| memory: "~{memory} GB" | ||
| cpu: cpu | ||
| disks: "local-disk ~{disk_size} SSD" | ||
| preemptible: 0 | ||
| } | ||
| } |
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