diff --git a/modules/umitools/dedup/meta.yml b/modules/umitools/dedup/meta.yml new file mode 100644 index 00000000..f89cc1ea --- /dev/null +++ b/modules/umitools/dedup/meta.yml @@ -0,0 +1,47 @@ +name: umitools_dedup +description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. +keywords: + - umitools + - deduplication +tools: + - umi_tools: + description: > + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) + and single cell RNA-Seq cell barcodes + documentation: https://umi-tools.readthedocs.io/en/latest/ + license: ['MIT'] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@drpatelh" + - "@grst" + - "@klkeys" diff --git a/modules/umitools/extract/meta.yml b/modules/umitools/extract/meta.yml new file mode 100644 index 00000000..ae6f9fee --- /dev/null +++ b/modules/umitools/extract/meta.yml @@ -0,0 +1,46 @@ +name: umitools_extract +description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place +keywords: + - umitools + - extract +tools: + - umi_tools: + description: > + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) + and single cell RNA-Seq cell barcodes + documentation: https://umi-tools.readthedocs.io/en/latest/ + license: ['MIT'] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FASTQ files whose UMIs will be extracted. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Extracted FASTQ files. | + For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | + For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + pattern: "*.{fastq.gz}" + - log: + type: file + description: Logfile for umi_tools + pattern: "*.{log}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@drpatelh" + - "@grst"