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add lane concatenation to theiaproks
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| version 1.0 | ||
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| task cat_lanes { | ||
| input { | ||
| String samplename | ||
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| File read1_lane1 | ||
| File read1_lane2 | ||
| File? read1_lane3 | ||
| File? read1_lane4 | ||
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| File? read2_lane1 | ||
| File? read2_lane2 | ||
| File? read2_lane3 | ||
| File? read2_lane4 | ||
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| Int cpu = 2 | ||
| Int disk_size = 50 | ||
| String docker = "us-docker.pkg.dev/general-theiagen/theiagen/utility:1.2" | ||
| Int memory = 4 | ||
| } | ||
| meta { | ||
| volatile: true | ||
| } | ||
| command <<< | ||
| # exit task if anything throws an error (important for proper gzip format) | ||
| set -euo pipefail | ||
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| # move reads into single directory | ||
| mkdir -v reads | ||
| mv -v ~{read1_lane1} \ | ||
| ~{read2_lane1} \ | ||
| ~{read1_lane2} \ | ||
| ~{read2_lane2} \ | ||
| ~{read1_lane3} \ | ||
| ~{read2_lane3} \ | ||
| ~{read1_lane4} \ | ||
| ~{read2_lane4} \ | ||
| reads/ | ||
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| # check for valid gzipped format (this task assumes FASTQ files are gzipped - they should be coming from ILMN instruments) | ||
| gzip -t reads/*.gz | ||
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| # run concatenate script and send STDOUT/ERR to STDOUT | ||
| # reminder: script will skip over samples that only have R1 file present | ||
| # reminder: script REQUIRES standard illumina file endings like: _L001_R1_001.fastq.gz and _L002_R2_001.fastq.gz | ||
| # see script here: https://github.com/theiagen/utilities/blob/main/scripts/concatenate-across-lanes.sh | ||
| concatenate-across-lanes.sh reads/ | ||
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| # ensure newly merged FASTQs are valid gzipped format | ||
| gzip -t reads/*merged*.gz | ||
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| # determine output filenames for outputs | ||
| mv -v reads/*_merged_R1.fastq.gz reads/~{samplename}_merged_R1.fastq.gz | ||
| mv -v reads/*_merged_R2.fastq.gz reads/~{samplename}_merged_R2.fastq.gz | ||
| >>> | ||
| output { | ||
| File read1_concatenated = "reads/~{samplename}_merged_R1.fastq.gz" | ||
| File? read2_concatenated = "reads/~{samplename}_merged_R2.fastq.gz" | ||
| } | ||
| runtime { | ||
| docker: "~{docker}" | ||
| memory: memory + " GB" | ||
| cpu: cpu | ||
| disks: "local-disk " + disk_size + " HDD" | ||
| disk: disk_size + " GB" | ||
| preemptible: 1 | ||
| } | ||
| } |
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42 changes: 42 additions & 0 deletions
42
workflows/utilities/file_handling/wf_concatenate_illumina_lanes.wdl
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,42 @@ | ||
| version 1.0 | ||
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| import "../../../tasks/utilities/file_handling/task_cat_lanes.wdl" as concatenate_lanes | ||
| import "../../../tasks/task_versioning.wdl" as versioning | ||
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| workflow concatenate_illumina_lanes { | ||
| input { | ||
| String samplename | ||
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| File read1_lane1 | ||
| File read1_lane2 | ||
| File? read1_lane3 | ||
| File? read1_lane4 | ||
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| File? read2_lane1 | ||
| File? read2_lane2 | ||
| File? read2_lane3 | ||
| File? read2_lane4 | ||
| } | ||
| call concatenate_lanes.cat_lanes { | ||
| input: | ||
| samplename = samplename, | ||
| read1_lane1 = read1_lane1, | ||
| read2_lane1 = read2_lane1, | ||
| read1_lane2 = read1_lane2, | ||
| read2_lane2 = read2_lane2, | ||
| read1_lane3 = read1_lane3, | ||
| read2_lane3 = read2_lane3, | ||
| read1_lane4 = read1_lane4, | ||
| read2_lane4 = read2_lane4 | ||
| } | ||
| call versioning.version_capture { | ||
| input: | ||
| } | ||
| output { | ||
| String concatenate_illumina_lanes_version = version_capture.phb_version | ||
| String concatenate_illumina_lanes_analysis_date = version_capture.date | ||
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| File read1_concatenated = cat_lanes.read1_concatenated | ||
| File? read2_concatenated = cat_lanes.read2_concatenated | ||
| } | ||
| } |