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* initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586b. * inital commit dedup * Working component with one test * Update test 1 and test data, fix some arg types in config and script * test data files and changes to script * Add third test and test data * Fix typo in script * remove utf8 characters in config * Add choices fields and change default fields to exampels * Minor formatting changes * md formatting changes in config
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,303 @@ | ||
| name: umi_tools_dedup | ||
| namespace: umi_tools | ||
| description: | | ||
| Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. | ||
| keywords: [umi_tools, deduplication, dedup] | ||
| links: | ||
| homepage: https://umi-tools.readthedocs.io/en/latest/ | ||
| documentation: https://umi-tools.readthedocs.io/en/latest/reference/dedup.html | ||
| repository: https://github.com/CGATOxford/UMI-tools | ||
| references: | ||
| doi: 10.1101/gr.209601.116 | ||
| license: MIT | ||
|
|
||
| argument_groups: | ||
| - name: Inputs | ||
| arguments: | ||
| - name: --input | ||
| alternatives: --stdin | ||
| type: file | ||
| description: Input BAM or SAM file. Use --in_sam to specify SAM format. | ||
| required: true | ||
| - name: --in_sam | ||
| type: boolean_true | ||
| description: | | ||
| By default, inputs are assumed to be in BAM format. Use this options to specify the use of SAM | ||
| format for input. | ||
| - name: --bai | ||
| type: file | ||
| description: BAM index | ||
| - name: --random_seed | ||
| type: integer | ||
| description: Random seed to initialize number generator with. | ||
|
|
||
| - name: Outputs | ||
| arguments: | ||
| - name: --output | ||
| alternatives: --stdout | ||
| type: file | ||
| description: Deduplicated BAM file. | ||
| required: true | ||
| direction: output | ||
| - name: --out_sam | ||
| type: boolean_true | ||
| description: | | ||
| By default, outputa are written in BAM format. Use this options to specify the use of SAM format | ||
| for output. | ||
| - name: --paired | ||
| type: boolean_true | ||
| description: | | ||
| BAM is paired end - output both read pairs. This will also force the use of the template length | ||
| to determine reads with the same mapping coordinates. | ||
| - name: --output_stats | ||
| type: string | ||
| description: | | ||
| Generate files containing UMI based deduplication statistics files with this prefix in the file names. | ||
| - name: --extract_umi_method | ||
| type: string | ||
| choices: [read_id, tag, umis] | ||
| description: | | ||
| Specify the method by which the barcodes were encoded in the read. | ||
| The options are: | ||
| * read_id (default) | ||
| * tag | ||
| * umis | ||
| example: "read_id" | ||
| - name: --umi_tag | ||
| type: string | ||
| description: | | ||
| The tag containing the UMI sequence. This is only required if the extract_umi_method is set to tag. | ||
| - name: --umi_separator | ||
| type: string | ||
| description: | | ||
| The separator used to separate the UMI from the read sequence. This is only required if the | ||
| extract_umi_method is set to id_read. Default: `_`. | ||
| example: '_' | ||
| - name: --umi_tag_split | ||
| type: string | ||
| description: Separate the UMI in tag by <SPLIT> and take the first element. | ||
| - name: --umi_tag_delimiter | ||
| type: string | ||
| description: Separate the UMI in by <DELIMITER> and concatenate the elements. | ||
| - name: --cell_tag | ||
| type: string | ||
| description: | | ||
| The tag containing the cell barcode sequence. This is only required if the extract_umi_method | ||
| is set to tag. | ||
| - name: --cell_tag_split | ||
| type: string | ||
| description: Separate the cell barcode in tag by <SPLIT> and take the first element. | ||
| - name: --cell_tag_delimiter | ||
| type: string | ||
| description: Separate the cell barcode in by <DELIMITER> and concatenate the elements. | ||
|
|
||
| - name: Grouping Options | ||
| arguments: | ||
| - name: --method | ||
| type: string | ||
| choices: [unique, percentile, cluster, adjacency, directional] | ||
| description: | | ||
| The method to use for grouping reads. | ||
| The options are: | ||
| * unique | ||
| * percentile | ||
| * cluster | ||
| * adjacency | ||
| * directional (default) | ||
| example: "directional" | ||
| - name: --edit_distance_threshold | ||
| type: integer | ||
| description: | | ||
| For the adjacency and cluster methods the threshold for the edit distance to connect two | ||
| UMIs in the network can be increased. The default value of 1 works best unless the UMI is | ||
| very long (>14bp). Default: `1`. | ||
| example: 1 | ||
| - name: --spliced_is_unique | ||
| type: boolean_true | ||
| description: | | ||
| Causes two reads that start in the same position on the same strand and having the same UMI | ||
| to be considered unique if one is spliced and the other is not. (Uses the 'N' cigar operation | ||
| to test for splicing). | ||
| - name: --soft_clip_threshold | ||
| type: integer | ||
| description: | | ||
| Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only | ||
| a small overhang over the exon junction. By setting this option, you can treat reads with at | ||
| least this many bases soft-clipped at the 3' end as spliced. Default: `4`. | ||
| example: 4 | ||
| - name: --multimapping_detection_method | ||
| type: string | ||
| description: | | ||
| If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting | ||
| the best read at a given loci. Supported tags are `NH`, `X0` and `XT`. If not specified, the read | ||
| with the highest mapping quality will be selected. | ||
| - name: --read_length | ||
| type: boolean_true | ||
| description: Use the read length as a criteria when deduping, for e.g. sRNA-Seq. | ||
|
|
||
| - name: Single-cell RNA-Seq Options | ||
| arguments: | ||
| - name: --per_gene | ||
| type: boolean_true | ||
| description: | | ||
| Reads will be grouped together if they have the same gene. This is useful if your library prep | ||
| generates PCR duplicates with non identical alignment positions such as CEL-Seq. Note this option | ||
| is hardcoded to be on with the count command. I.e. counting is always performed per-gene. Must be | ||
| combined with either --gene_tag or --per_contig option. | ||
| - name: --gene_tag | ||
| type: string | ||
| description: | | ||
| Deduplicate per gene. The gene information is encoded in the bam read tag specified. | ||
| - name: --assigned_status_tag | ||
| type: string | ||
| description: | | ||
| BAM tag which describes whether a read is assigned to a gene. Defaults to the same value as given | ||
| for --gene_tag. | ||
| - name: --skip_tags_regex | ||
| type: string | ||
| description: | | ||
| Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches | ||
| this regex. Default ("^[__|Unassigned]") matches anything which starts with "__" or "Unassigned". | ||
| - name: --per_contig | ||
| type: boolean_true | ||
| description: | | ||
| Deduplicate per contig (field 3 in BAM; RNAME). All reads with the sam contig will be considered to | ||
| have the same alignment position. This is useful if you have aligned to a reference transcriptome | ||
| with one transcript per gene. If you have aligned to a transcriptome with more than one transcript | ||
| per gene, you can supply a map between transcripts and gene using the --gene_transcript_map option. | ||
| - name: --gene_transcript_map | ||
| type: file | ||
| description: | | ||
| A file containing a mapping between gene names and transcript names. The file should be tab | ||
| separated with the gene name in the first column and the transcript name in the second column. | ||
| - name: --per_cell | ||
| type: boolean_true | ||
| description: | | ||
| Reads will only be grouped together if they have the same cell barcode. Can be combined with | ||
| --per_gene. | ||
| - name: SAM/BAM Options | ||
| arguments: | ||
| - name: --mapping_quality | ||
| type: integer | ||
| description: | | ||
| Minimium mapping quality (MAPQ) for a read to be retained. Default: `0`. | ||
| example: 0 | ||
| - name: --unmapped_reads | ||
| type: string | ||
| description: | | ||
| How unmapped reads should be handled. | ||
| The options are: | ||
| * "discard": Discard all unmapped reads. (default) | ||
| * "use": If read2 is unmapped, deduplicate using read1 only. Requires --paired. | ||
| * "output": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group. | ||
| example: "discard" | ||
| - name: --chimeric_pairs | ||
| type: string | ||
| choices: [discard, use, output] | ||
| description: | | ||
| How chimeric pairs should be handled. | ||
| The options are: | ||
| * "discard": Discard all chimeric read pairs. | ||
| * "use": Deduplicate using read1 only. (default) | ||
| * "output": Output chimeric pairs without UMI grouping/deduplication. Only available in | ||
| umi_tools group. | ||
| example: "use" | ||
| - name: --unpaired_reads | ||
| type: string | ||
| choices: [discard, use, output] | ||
| description: | | ||
| How unpaired reads should be handled. | ||
| The options are: | ||
| * "discard": Discard all unmapped reads. | ||
| * "use": If read2 is unmapped, deduplicate using read1 only. Requires --paired. (default) | ||
| * "output": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available | ||
| in umi_tools group. | ||
| example: "use" | ||
| - name: --ignore_umi | ||
| type: boolean_true | ||
| description: Ignore the UMI and group reads using mapping coordinates only. | ||
| - name: --subset | ||
| type: double | ||
| description: | | ||
| Only consider a fraction of the reads, chosen at random. This is useful for doing saturation | ||
| analyses. | ||
| - name: --chrom | ||
| type: string | ||
| description: Only consider a single chromosome. This is useful for debugging/testing purposes. | ||
|
|
||
| - name: Group/Dedup Options | ||
| arguments: | ||
| - name: --no_sort_output | ||
| type: boolean_true | ||
| description: | | ||
| By default, output is sorted. This involves the use of a temporary unsorted file (saved in | ||
| --temp_dir). Use this option to turn off sorting. | ||
| - name: --buffer_whole_contig | ||
| type: boolean_true | ||
| description: | | ||
| Forces dedup to parse an entire contig before yielding any reads for deduplication. This is the | ||
| only way to absolutely guarantee that all reads with the same start position are grouped together | ||
| for deduplication since dedup uses the start position of the read, not the alignment coordinate on | ||
| which the reads are sorted. However, by default, dedup reads for another 1000bp before outputting | ||
| read groups which will avoid any reads being missed with short read sequencing (<1000bp). | ||
| - name: Common Options | ||
| arguments: | ||
| - name: --log | ||
| alternatives: -L | ||
| type: file | ||
| description: File with logging information. | ||
| - name: --log2stderr | ||
| type: boolean_true | ||
| description: Send logging information to stderr. | ||
| - name: --verbose | ||
| alternatives: -v | ||
| type: integer | ||
| description: | | ||
| Log level. The higher, the more output. Default: `0`. | ||
| example: 0 | ||
| - name: --error | ||
| alternatives: -E | ||
| type: file | ||
| description: File with error information. | ||
| - name: --temp_dir | ||
| type: string | ||
| description: | | ||
| Directory for temporary files. If not set, the bash environmental variable TMPDIR is used. | ||
| - name: --compresslevel | ||
| type: integer | ||
| description: | | ||
| Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default. | ||
| Default: `6`. | ||
| example: 6 | ||
| - name: --timeit | ||
| type: file | ||
| description: Store timing information in file. | ||
| - name: --timeit_name | ||
| type: string | ||
| description: | | ||
| Name in timing file for this class of jobs. Default: `all`. | ||
| example: "all" | ||
| - name: --timeit_header | ||
| type: string | ||
| description: Add header for timing information. | ||
|
|
||
| resources: | ||
| - type: bash_script | ||
| path: script.sh | ||
| test_resources: | ||
| - type: bash_script | ||
| path: test.sh | ||
| - type: file | ||
| path: test_data | ||
| engines: | ||
| - type: docker | ||
| image: quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1 | ||
| setup: | ||
| - type: docker | ||
| run: | | ||
| umi_tools -v | sed 's/ version//g' > /var/software_versions.txt | ||
| runners: | ||
| - type: executable | ||
| - type: nextflow |
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